From 970379f2dc53d7390878eb8d68394870ede815c5 Mon Sep 17 00:00:00 2001 From: Johannes Linder Date: Mon, 30 Sep 2024 09:46:50 -0700 Subject: [PATCH] Revision updates. --- download_models.sh | 68 + env_vars.sh | 50 + examples/CD99_example.gtf | 156 + examples/CFHR2_example.gtf | 15 + examples/GCFC2_example.gtf | 126 + ...zoi_example_eqtl_chr10_116952944_T_C.ipynb | 166 +- ...i_example_ipaqtl_chr10_116664061_G_A.ipynb | 128 +- ...zoi_example_paqtl_chr1_236763042_A_G.ipynb | 128 +- ...rzoi_example_sqtl_chr9_135548708_G_C.ipynb | 126 +- examples/params.json | 87 + examples/params_pred.json | 58 +- examples/targets_gtex_liver.txt | 4 + examples/targets_mouse.txt | 2609 +++++++++++++++++ examples/targets_rna.txt | 1544 ++++++++++ pyproject.toml | 43 +- setup.cfg | 43 - .../{ => _archive}/borzoi_bench_crispr.py | 0 .../borzoi_bench_crispr_folds.py | 0 .../borzoi_bench_flowfish_folds.py | 0 .../borzoi_bench_gasperini_folds.py | 0 src/scripts/_archive/borzoi_satg_gene.py | 351 +++ .../{ => _archive}/borzoi_satg_gene_multi.py | 0 ...h_classify.py => borzoi_bench_classify.py} | 2 +- ...olds.py => borzoi_bench_gtex_folds_sad.py} | 27 +- ...olds.py => borzoi_bench_gtex_folds_sed.py} | 19 +- src/scripts/borzoi_bench_ipaqtl_folds.py | 13 +- src/scripts/borzoi_bench_paqtl_folds.py | 13 +- src/scripts/borzoi_bench_sqtl_folds.py | 12 +- src/scripts/borzoi_bench_trip_folds.py | 6 +- ...i_gtex_coef.py => borzoi_gtex_coef_sad.py} | 15 +- ...i_gtex_coef.py => borzoi_gtex_coef_sed.py} | 15 +- src/scripts/{basenji_sad.py => borzoi_sad.py} | 4 +- src/scripts/borzoi_sad_folds.py | 266 ++ src/scripts/borzoi_satg_gene.py | 821 +++++- ...=> borzoi_satg_gene_crispr_ism_shuffle.py} | 15 +- ...ism.py => borzoi_satg_gene_focused_ism.py} | 15 +- src/scripts/borzoi_satg_gene_gpu.py | 903 ------ ...satg_polya_gpu.py => borzoi_satg_polya.py} | 17 +- ...tg_splice_gpu.py => borzoi_satg_splice.py} | 17 +- src/scripts/borzoi_sed.py | 4 +- src/scripts/borzoi_sed_folds.py | 8 +- src/scripts/borzoi_sed_ipaqtl_cov.py | 7 +- src/scripts/borzoi_sed_paqtl_cov.py | 7 +- ...test_apa_polaydb.py => borzoi_test_apa.py} | 10 +- ...ds_polaydb.py => borzoi_test_apa_folds.py} | 13 +- src/scripts/borzoi_test_exons.py | 22 +- src/scripts/borzoi_test_exons_folds.py | 36 +- src/scripts/borzoi_test_genes.py | 2 +- src/scripts/borzoi_test_genes_folds.py | 6 +- ...test_tss_gencode.py => borzoi_test_tss.py} | 10 +- ...ds_gencode.py => borzoi_test_tss_folds.py} | 13 +- src/scripts/borzoi_tfmodisco.py | 6 +- src/scripts/borzoi_tfmodisco_diff.py | 6 +- src/scripts/borzoi_trip.py | 4 +- src/scripts/bw_h5.py | 140 + src/scripts/data/qtl_data/README.md | 33 - src/scripts/data/qtl_data/download_finemap.py | 62 - src/scripts/data/qtl_data/download_sumstat.py | 56 - .../qtl_data/ipaqtl_make_negative_sets.py | 196 -- .../qtl_data/ipaqtl_make_positive_sets.py | 191 -- src/scripts/data/qtl_data/ipaqtl_vcfs.py | 234 -- .../data/qtl_data/make_expression_tables.py | 181 -- src/scripts/data/qtl_data/make_vcfs.py | 112 - .../data/qtl_data/merge_finemapping_tables.py | 102 - .../data/qtl_data/paqtl_make_negative_sets.py | 196 -- .../data/qtl_data/paqtl_make_positive_sets.py | 191 -- src/scripts/data/qtl_data/paqtl_vcfs.py | 234 -- .../data/qtl_data/sqtl_make_negative_sets.py | 195 -- .../data/qtl_data/sqtl_make_positive_sets.py | 190 -- src/scripts/data/qtl_data/sqtl_vcfs.py | 234 -- src/scripts/data/training_data/Makefile | 47 - src/scripts/data/training_data/README.md | 11 - src/scripts/idx_genome.py | 32 + src/scripts/pygene.py | 324 ++ src/scripts/slurm.py | 332 +++ src/scripts/util.py | 120 + src/scripts/w5_merge.py | 110 + src/scripts/w5_qc.py | 322 ++ 78 files changed, 7941 insertions(+), 3940 deletions(-) create mode 100755 download_models.sh create mode 100755 env_vars.sh create mode 100644 examples/CD99_example.gtf create mode 100644 examples/CFHR2_example.gtf create mode 100644 examples/GCFC2_example.gtf create mode 100644 examples/params.json create mode 100644 examples/targets_gtex_liver.txt create mode 100644 examples/targets_mouse.txt create mode 100644 examples/targets_rna.txt delete mode 100644 setup.cfg rename src/scripts/{ => _archive}/borzoi_bench_crispr.py (100%) rename src/scripts/{ => _archive}/borzoi_bench_crispr_folds.py (100%) rename src/scripts/{ => _archive}/borzoi_bench_flowfish_folds.py (100%) rename src/scripts/{ => _archive}/borzoi_bench_gasperini_folds.py (100%) create mode 100755 src/scripts/_archive/borzoi_satg_gene.py rename src/scripts/{ => _archive}/borzoi_satg_gene_multi.py (100%) rename src/scripts/{basenji_bench_classify.py => borzoi_bench_classify.py} (99%) mode change 100644 => 100755 rename src/scripts/{basenji_bench_gtex_folds.py => borzoi_bench_gtex_folds_sad.py} (96%) mode change 100644 => 100755 rename src/scripts/{borzoi_bench_gtex_folds.py => borzoi_bench_gtex_folds_sed.py} (97%) mode change 100644 => 100755 rename src/scripts/{basenji_gtex_coef.py => borzoi_gtex_coef_sad.py} (96%) mode change 100644 => 100755 rename src/scripts/{borzoi_gtex_coef.py => borzoi_gtex_coef_sed.py} (97%) mode change 100644 => 100755 rename src/scripts/{basenji_sad.py => borzoi_sad.py} (99%) mode change 100644 => 100755 create mode 100755 src/scripts/borzoi_sad_folds.py rename src/scripts/{borzoi_satg_gene_gpu_crispr_ism_shuffle.py => borzoi_satg_gene_crispr_ism_shuffle.py} (98%) mode change 100644 => 100755 rename src/scripts/{borzoi_satg_gene_gpu_focused_ism.py => borzoi_satg_gene_focused_ism.py} (98%) delete mode 100755 src/scripts/borzoi_satg_gene_gpu.py rename src/scripts/{borzoi_satg_polya_gpu.py => borzoi_satg_polya.py} (98%) rename src/scripts/{borzoi_satg_splice_gpu.py => borzoi_satg_splice.py} (98%) mode change 100644 => 100755 src/scripts/borzoi_sed_folds.py rename src/scripts/{borzoi_test_apa_polaydb.py => borzoi_test_apa.py} (97%) rename src/scripts/{borzoi_test_apa_folds_polaydb.py => borzoi_test_apa_folds.py} (93%) rename src/scripts/{borzoi_test_tss_gencode.py => borzoi_test_tss.py} (96%) mode change 100644 => 100755 rename src/scripts/{borzoi_test_tss_folds_gencode.py => borzoi_test_tss_folds.py} (94%) mode change 100644 => 100755 mode change 100644 => 100755 src/scripts/borzoi_tfmodisco.py mode change 100644 => 100755 src/scripts/borzoi_tfmodisco_diff.py create mode 100755 src/scripts/bw_h5.py delete mode 100644 src/scripts/data/qtl_data/README.md delete mode 100644 src/scripts/data/qtl_data/download_finemap.py delete mode 100644 src/scripts/data/qtl_data/download_sumstat.py delete mode 100644 src/scripts/data/qtl_data/ipaqtl_make_negative_sets.py delete mode 100644 src/scripts/data/qtl_data/ipaqtl_make_positive_sets.py delete mode 100644 src/scripts/data/qtl_data/ipaqtl_vcfs.py delete mode 100644 src/scripts/data/qtl_data/make_expression_tables.py delete mode 100644 src/scripts/data/qtl_data/make_vcfs.py delete mode 100644 src/scripts/data/qtl_data/merge_finemapping_tables.py delete mode 100644 src/scripts/data/qtl_data/paqtl_make_negative_sets.py delete mode 100644 src/scripts/data/qtl_data/paqtl_make_positive_sets.py delete mode 100644 src/scripts/data/qtl_data/paqtl_vcfs.py delete mode 100644 src/scripts/data/qtl_data/sqtl_make_negative_sets.py delete mode 100644 src/scripts/data/qtl_data/sqtl_make_positive_sets.py delete mode 100644 src/scripts/data/qtl_data/sqtl_vcfs.py delete mode 100644 src/scripts/data/training_data/Makefile delete mode 100644 src/scripts/data/training_data/README.md create mode 100755 src/scripts/idx_genome.py create mode 100755 src/scripts/pygene.py create mode 100755 src/scripts/slurm.py create mode 100755 src/scripts/util.py create mode 100755 src/scripts/w5_merge.py create mode 100755 src/scripts/w5_qc.py diff --git a/download_models.sh b/download_models.sh new file mode 100755 index 0000000..1ec7a26 --- /dev/null +++ b/download_models.sh @@ -0,0 +1,68 @@ +#!/bin/bash + +# download model weights (data fold 3, 4 replicates) +for rep in f3c0,f0 f3c1,f1 f3c2,f2 f3c3,f3; do IFS=","; set -- $rep; + mkdir -p "examples/saved_models/$1/train" + local_model="examples/saved_models/$1/train/model0_best.h5" + if [ -f "$local_model" ]; then + echo "$1 model already exists." + else + wget --progress=bar:force "https://storage.googleapis.com/seqnn-share/borzoi/$2/model0_best.h5" -O "$local_model" + fi +done + +# download and uncompress annotation files +mkdir -p examples/hg38/genes/gencode41 +mkdir -p examples/hg38/genes/polyadb + +if [ -f examples/hg38/genes/gencode41/gencode41_basic_nort.gtf ]; then + echo "Gene annotation already exists." +else + wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > examples/hg38/genes/gencode41/gencode41_basic_nort.gtf +fi + +if [ -f examples/hg38/genes/gencode41/gencode41_basic_nort_protein.gtf ]; then + echo "Gene annotation (no read-through, protein-coding) already exists." +else + wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort_protein.gtf.gz | gunzip -c > examples/hg38/genes/gencode41/gencode41_basic_nort_protein.gtf +fi + +if [ -f examples/hg38/genes/gencode41/gencode41_basic_protein.gtf ]; then + echo "Gene annotation (protein-coding) already exists." +else + wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein.gtf.gz | gunzip -c > examples/hg38/genes/gencode41/gencode41_basic_protein.gtf +fi + +if [ -f examples/hg38/genes/gencode41/gencode41_basic_tss2.bed ]; then + echo "TSS annotation already exists." +else + wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_tss2.bed.gz | gunzip -c > examples/hg38/genes/gencode41/gencode41_basic_tss2.bed +fi + +if [ -f examples/hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz ]; then + echo "Splice site annotation already exist." +else + wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz -O examples/hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz +fi + +if [ -f examples/hg38/genes/gencode41/gencode41_basic_protein_splice.gff ]; then + echo "Splice site annotation already exist." +else + wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.gff.gz | gunzip -c > examples/hg38/genes/gencode41/gencode41_basic_protein_splice.gff +fi + +if [ -f examples/hg38/genes/polyadb/polyadb_human_v3.csv.gz ]; then + echo "PolyA site annotation already exist." +else + wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz -O examples/hg38/genes/polyadb/polyadb_human_v3.csv.gz +fi + +# download and index hg38 genome +mkdir -p examples/hg38/assembly/ucsc + +if [ -f examples/hg38/assembly/ucsc/hg38.fa ]; then + echo "Human genome FASTA already exists." +else + wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > examples/hg38/assembly/ucsc/hg38.fa + python src/scripts/idx_genome.py examples/hg38/assembly/ucsc/hg38.fa +fi diff --git a/env_vars.sh b/env_vars.sh new file mode 100755 index 0000000..8d41e18 --- /dev/null +++ b/env_vars.sh @@ -0,0 +1,50 @@ +#!/bin/bash + +# set these variables before running the script +LOCAL_BORZOI_PATH="/home/jlinder/borzoi" +LOCAL_BASKERVILLE_PATH="/home/jlinder/baskerville" +LOCAL_WESTMINSTER_PATH="/home/jlinder/westminster" +LOCAL_USER="jlinder" + +# create env_vars sh scripts in local conda env +mkdir -p "$CONDA_PREFIX/etc/conda/activate.d" +mkdir -p "$CONDA_PREFIX/etc/conda/deactivate.d" + +file_vars_act="$CONDA_PREFIX/etc/conda/activate.d/env_vars.sh" +if ! [ -e $file_vars_act ]; then + echo '#!/bin/sh' > $file_vars_act +fi + +file_vars_deact="$CONDA_PREFIX/etc/conda/deactivate.d/env_vars.sh" +if ! [ -e $file_vars_deact ]; then + echo '#!/bin/sh' > $file_vars_deact +fi + +# append borzoi (and baskerville/westminster) env variable exports to /activate.d/env_vars.sh +echo "export BORZOI_DIR=$LOCAL_BORZOI_PATH" >> $file_vars_act +echo 'export PATH=$BORZOI_DIR/src/scripts:$PATH' >> $file_vars_act +echo 'export PYTHONPATH=$BORZOI_DIR/src/scripts:$PYTHONPATH' >> $file_vars_act + +echo "export BASKERVILLE_DIR=$LOCAL_BASKERVILLE_PATH" >> $file_vars_act +echo 'export PATH=$BASKERVILLE_DIR/src/baskerville/scripts:$PATH' >> $file_vars_act +echo 'export PYTHONPATH=$BASKERVILLE_DIR/src/baskerville/scripts:$PYTHONPATH' >> $file_vars_act + +echo "export WESTMINSTER_DIR=$LOCAL_WESTMINSTER_PATH" >> $file_vars_act +echo 'export PATH=$WESTMINSTER_DIR/src/westminster/scripts:$PATH' >> $file_vars_act +echo 'export PYTHONPATH=$WESTMINSTER_DIR/src/westminster/scripts:$PYTHONPATH' >> $file_vars_act + +echo 'export BORZOI_HG38=$BORZOI_DIR/examples/hg38' >> $file_vars_act +echo 'export BORZOI_MM10=$BORZOI_DIR/examples/mm10' >> $file_vars_act + +echo "export BORZOI_CONDA=/home/$LOCAL_USER/anaconda3/etc/profile.d/conda.sh" >> $file_vars_act + +# append borzoi env variable unsets to /deactivate.d/env_vars.sh +echo 'unset BASKERVILLE_DIR' >> $file_vars_deact +echo 'unset WESTMINSTER_DIR' >> $file_vars_deact +echo 'unset BORZOI_DIR' >> $file_vars_deact +echo 'unset BORZOI_HG38' >> $file_vars_deact +echo 'unset BORZOI_MM10' >> $file_vars_deact +echo 'unset BORZOI_CONDA' >> $file_vars_deact + +# finally activate env variables +source $file_vars_act diff --git a/examples/CD99_example.gtf b/examples/CD99_example.gtf new file mode 100644 index 0000000..7fc53a4 --- /dev/null +++ b/examples/CD99_example.gtf @@ -0,0 +1,156 @@ +chrX ENSEMBL transcript 2691187 2741300 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2691187 2691427 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 1; exon_id "ENSE00003729830.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2691361 2691427 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 1; exon_id "ENSE00003729830.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL start_codon 2691361 2691363 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 1; exon_id "ENSE00003729830.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2714422 2714454 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 2; exon_id "ENSE00003535342.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2714422 2714454 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 2; exon_id "ENSE00003535342.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2717605 2717652 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 3; exon_id "ENSE00003474982.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2717605 2717652 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 3; exon_id "ENSE00003474982.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2719661 2719705 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 4; exon_id "ENSE00003586106.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2719661 2719705 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 4; exon_id "ENSE00003586106.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2720356 2720424 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 5; exon_id "ENSE00003578821.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2720356 2720424 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 5; exon_id "ENSE00003578821.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2722627 2722674 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 6; exon_id "ENSE00003552837.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2722627 2722674 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 6; exon_id "ENSE00003552837.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2723314 2723364 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 7; exon_id "ENSE00003612985.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2723314 2723364 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 7; exon_id "ENSE00003612985.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2726260 2726373 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 8; exon_id "ENSE00003785141.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2726260 2726373 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 8; exon_id "ENSE00003785141.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2733357 2733374 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 9; exon_id "ENSE00003715936.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL CDS 2733357 2733361 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 9; exon_id "ENSE00003715936.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL stop_codon 2733362 2733364 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 9; exon_id "ENSE00003715936.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2738203 2738256 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 10; exon_id "ENSE00003720441.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL exon 2740779 2741300 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 11; exon_id "ENSE00003713358.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL UTR 2691187 2691360 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 1; exon_id "ENSE00003729830.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL UTR 2733362 2733374 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 9; exon_id "ENSE00003715936.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL UTR 2738203 2738256 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 10; exon_id "ENSE00003720441.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX ENSEMBL UTR 2740779 2741300 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000611428.5"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-210"; exon_number 11; exon_id "ENSE00003713358.1"; level 3; protein_id "ENSP00000479999.1"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; +chrX HAVANA transcript 2691276 2741101 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2691276 2691427 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 1; exon_id "ENSE00001870387.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2691361 2691427 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 1; exon_id "ENSE00001870387.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA start_codon 2691361 2691363 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 1; exon_id "ENSE00001870387.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2714422 2714454 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2714422 2714454 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2719661 2719705 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 3; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2719661 2719705 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 3; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2720356 2720424 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 4; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2720356 2720424 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 4; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2722627 2722674 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 5; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2722627 2722674 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 5; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2723314 2723364 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 6; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2723314 2723364 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 6; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2726260 2726373 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 7; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2726260 2726373 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 7; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2738200 2738256 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 8; exon_id "ENSE00001032174.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2738200 2738256 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 8; exon_id "ENSE00001032174.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA exon 2740779 2741101 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 9; exon_id "ENSE00001887497.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA CDS 2740779 2740801 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 9; exon_id "ENSE00001887497.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA stop_codon 2740802 2740804 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 9; exon_id "ENSE00001887497.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA UTR 2691276 2691360 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 1; exon_id "ENSE00001870387.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA UTR 2740802 2741101 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381187.8"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-204"; exon_number 9; exon_id "ENSE00001887497.1"; level 2; protein_id "ENSP00000370582.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS48071.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055626.1"; +chrX HAVANA transcript 2691280 2733667 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2691280 2691427 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 1; exon_id "ENSE00001487750.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2691361 2691427 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 1; exon_id "ENSE00001487750.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA start_codon 2691361 2691363 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 1; exon_id "ENSE00001487750.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2714422 2714454 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2714422 2714454 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2717605 2717652 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2717605 2717652 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2719661 2719705 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2719661 2719705 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2720356 2720424 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2720356 2720424 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2722627 2722674 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2722627 2722674 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2723314 2723364 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2723314 2723364 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2726260 2726373 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2726260 2726373 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2727293 2727343 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 9; exon_id "ENSE00001487748.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2727293 2727343 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 9; exon_id "ENSE00001487748.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA exon 2733357 2733667 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 10; exon_id "ENSE00001487747.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA CDS 2733357 2733361 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 10; exon_id "ENSE00001487747.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA stop_codon 2733362 2733364 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 10; exon_id "ENSE00001487747.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA UTR 2691280 2691360 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 1; exon_id "ENSE00001487750.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA UTR 2733362 2733667 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381184.6"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-203"; exon_number 10; exon_id "ENSE00001487747.1"; level 2; protein_id "ENSP00000370579.1"; transcript_support_level "5"; hgnc_id "HGNC:7082"; tag "non_canonical_TEC"; tag "dotter_confirmed"; tag "basic"; tag "appris_alternative_2"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055627.1"; +chrX HAVANA transcript 2691295 2741309 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2691295 2691427 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 1; exon_id "ENSE00001487792.5"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2691361 2691427 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 1; exon_id "ENSE00001487792.5"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA start_codon 2691361 2691363 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 1; exon_id "ENSE00001487792.5"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2714422 2714454 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2714422 2714454 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2717605 2717652 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2717605 2717652 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2719661 2719705 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2719661 2719705 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2720356 2720424 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2720356 2720424 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2722627 2722674 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2722627 2722674 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2723314 2723364 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2723314 2723364 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2726260 2726373 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2726260 2726373 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2738200 2738256 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 9; exon_id "ENSE00001032174.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2738200 2738256 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 9; exon_id "ENSE00001032174.1"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA exon 2740779 2741309 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 10; exon_id "ENSE00001487771.3"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA CDS 2740779 2740801 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 10; exon_id "ENSE00001487771.3"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA stop_codon 2740802 2740804 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 10; exon_id "ENSE00001487771.3"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA UTR 2691295 2691360 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 1; exon_id "ENSE00001487792.5"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA UTR 2740802 2741309 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381192.10"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-205"; exon_number 10; exon_id "ENSE00001487771.3"; level 2; protein_id "ENSP00000370588.3"; transcript_support_level "1"; hgnc_id "HGNC:7082"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_4"; tag "CCDS"; ccdsid "CCDS14119.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055624.3"; +chrX HAVANA transcript 2691310 2733672 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2691310 2691427 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 1; exon_id "ENSE00003331907.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2691361 2691427 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 1; exon_id "ENSE00003331907.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA start_codon 2691361 2691363 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 1; exon_id "ENSE00003331907.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2714422 2714454 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2714422 2714454 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2717605 2717652 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2717605 2717652 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2719661 2719705 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2719661 2719705 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2720356 2720424 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2720356 2720424 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2722627 2722674 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2722627 2722674 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2723314 2723364 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2723314 2723364 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2726260 2726373 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2726260 2726373 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA exon 2733357 2733672 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 9; exon_id "ENSE00001862861.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA CDS 2733357 2733361 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 9; exon_id "ENSE00001862861.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA stop_codon 2733362 2733364 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 9; exon_id "ENSE00001862861.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA UTR 2691310 2691360 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 1; exon_id "ENSE00003331907.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA UTR 2733362 2733672 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000482405.7"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-208"; exon_number 9; exon_id "ENSE00001862861.1"; level 2; protein_id "ENSP00000494027.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS75947.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000087928.3"; +chrX HAVANA transcript 2691313 2741290 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2691313 2691427 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 1; exon_id "ENSE00003755750.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2691361 2691427 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 1; exon_id "ENSE00003755750.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA start_codon 2691361 2691363 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 1; exon_id "ENSE00003755750.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2714422 2714454 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2714422 2714454 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 2; exon_id "ENSE00003535342.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2717605 2717652 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2717605 2717652 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 3; exon_id "ENSE00003474982.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2719661 2719705 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2719661 2719705 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 4; exon_id "ENSE00003586106.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2720356 2720424 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2720356 2720424 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 5; exon_id "ENSE00003578821.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2722627 2722674 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2722627 2722674 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 6; exon_id "ENSE00003552837.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2723314 2723364 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2723314 2723364 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 7; exon_id "ENSE00003612985.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2726260 2726373 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2726260 2726373 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 8; exon_id "ENSE00003785141.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2738203 2738256 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 9; exon_id "ENSE00003758767.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2738203 2738256 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 9; exon_id "ENSE00003758767.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA exon 2740779 2741290 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 10; exon_id "ENSE00003758362.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA CDS 2740779 2740801 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 10; exon_id "ENSE00003758362.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA stop_codon 2740802 2740804 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 10; exon_id "ENSE00003758362.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA UTR 2691313 2691360 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 1; exon_id "ENSE00003755750.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA UTR 2740802 2741290 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000624481.4"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-212"; exon_number 10; exon_id "ENSE00003758362.1"; level 2; protein_id "ENSP00000485427.1"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "NAGNAG_splice_site"; tag "basic"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS83452.1"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000478890.1"; +chrX HAVANA transcript 2691361 2692253 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; +chrX HAVANA exon 2691361 2691427 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; exon_number 1; exon_id "ENSE00001902734.1"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; +chrX HAVANA CDS 2691361 2691427 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; exon_number 1; exon_id "ENSE00001902734.1"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; +chrX HAVANA start_codon 2691361 2691363 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; exon_number 1; exon_id "ENSE00001902734.1"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; +chrX HAVANA exon 2691788 2692253 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; exon_number 2; exon_id "ENSE00001669439.3"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; +chrX HAVANA CDS 2691788 2691948 . + 2 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; exon_number 2; exon_id "ENSE00001669439.3"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; +chrX HAVANA stop_codon 2691949 2691951 . + 0 gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; exon_number 2; exon_id "ENSE00001669439.3"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; +chrX HAVANA UTR 2691949 2692253 . + . gene_id "ENSG00000002586.20"; transcript_id "ENST00000381180.9"; gene_type "protein_coding"; gene_name "CD99"; transcript_type "protein_coding"; transcript_name "CD99-202"; exon_number 2; exon_id "ENSE00001669439.3"; level 2; protein_id "ENSP00000370573.3"; transcript_support_level "2"; hgnc_id "HGNC:7082"; tag "basic"; havana_gene "OTTHUMG00000021073.12"; havana_transcript "OTTHUMT00000055625.2"; diff --git a/examples/CFHR2_example.gtf b/examples/CFHR2_example.gtf new file mode 100644 index 0000000..82ccfff --- /dev/null +++ b/examples/CFHR2_example.gtf @@ -0,0 +1,15 @@ +chr1 HAVANA transcript 196943738 196959622 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA exon 196943738 196943938 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 1; exon_id "ENSE00001920108.3"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA CDS 196943881 196943938 . + 0 gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 1; exon_id "ENSE00001920108.3"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA start_codon 196943881 196943883 . + 0 gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 1; exon_id "ENSE00001920108.3"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA exon 196949455 196949649 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 2; exon_id "ENSE00003745979.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA CDS 196949455 196949649 . + 2 gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 2; exon_id "ENSE00003745979.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA exon 196950852 196951028 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 3; exon_id "ENSE00003831930.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA CDS 196950852 196951028 . + 2 gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 3; exon_id "ENSE00003831930.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA exon 196957891 196958073 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 4; exon_id "ENSE00003836915.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA CDS 196957891 196958073 . + 2 gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 4; exon_id "ENSE00003836915.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA exon 196958881 196959622 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 5; exon_id "ENSE00003843688.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA CDS 196958881 196959077 . + 2 gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 5; exon_id "ENSE00003843688.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA stop_codon 196959078 196959080 . + 0 gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 5; exon_id "ENSE00003843688.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA UTR 196943738 196943880 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 1; exon_id "ENSE00001920108.3"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; +chr1 HAVANA UTR 196959078 196959622 . + . gene_id "ENSG00000080910.14"; transcript_id "ENST00000367415.8"; gene_type "protein_coding"; gene_name "CFHR2"; transcript_type "protein_coding"; transcript_name "CFHR2-201"; exon_number 5; exon_id "ENSE00003843688.1"; level 2; protein_id "ENSP00000356385.4"; transcript_support_level "1"; hgnc_id "HGNC:4890"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS30959.1"; havana_gene "OTTHUMG00000036518.4"; havana_transcript "OTTHUMT00000088815.4"; diff --git a/examples/GCFC2_example.gtf b/examples/GCFC2_example.gtf new file mode 100644 index 0000000..f271f76 --- /dev/null +++ b/examples/GCFC2_example.gtf @@ -0,0 +1,126 @@ +chr2 HAVANA transcript 75662705 75710915 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75710591 75710915 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 1; exon_id "ENSE00001261900.4"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75710591 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 1; exon_id "ENSE00001261900.4"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA start_codon 75710853 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 1; exon_id "ENSE00001261900.4"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75706523 75706651 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 2; exon_id "ENSE00003651464.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75706523 75706651 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 2; exon_id "ENSE00003651464.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75702199 75702423 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 3; exon_id "ENSE00003608878.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75702199 75702423 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 3; exon_id "ENSE00003608878.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75701190 75701287 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 4; exon_id "ENSE00003668748.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75701190 75701287 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 4; exon_id "ENSE00003668748.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75696200 75696315 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 5; exon_id "ENSE00003492242.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75696200 75696315 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 5; exon_id "ENSE00003492242.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75694241 75694427 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 6; exon_id "ENSE00003663933.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75694241 75694427 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 6; exon_id "ENSE00003663933.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75691977 75692100 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 7; exon_id "ENSE00003535454.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75691977 75692100 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 7; exon_id "ENSE00003535454.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75690638 75690719 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 8; exon_id "ENSE00003556420.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75690638 75690719 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 8; exon_id "ENSE00003556420.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75689969 75690081 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 9; exon_id "ENSE00003593081.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75689969 75690081 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 9; exon_id "ENSE00003593081.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75689026 75689225 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 10; exon_id "ENSE00003615519.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75689026 75689225 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 10; exon_id "ENSE00003615519.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75687827 75687977 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 11; exon_id "ENSE00003566359.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75687827 75687977 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 11; exon_id "ENSE00003566359.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75680193 75680314 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 12; exon_id "ENSE00003522865.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75680193 75680314 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 12; exon_id "ENSE00003522865.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75673444 75673520 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 13; exon_id "ENSE00003474620.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75673444 75673520 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 13; exon_id "ENSE00003474620.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75671950 75672016 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 14; exon_id "ENSE00003475605.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75671950 75672016 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 14; exon_id "ENSE00003475605.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75670138 75670284 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 15; exon_id "ENSE00003563051.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75670138 75670284 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 15; exon_id "ENSE00003563051.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75665929 75666053 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 16; exon_id "ENSE00003582023.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75665929 75666053 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 16; exon_id "ENSE00003582023.1"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA exon 75662705 75664783 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 17; exon_id "ENSE00003465078.2"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA CDS 75664669 75664783 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 17; exon_id "ENSE00003465078.2"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA stop_codon 75664666 75664668 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 17; exon_id "ENSE00003465078.2"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA UTR 75710856 75710915 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 1; exon_id "ENSE00001261900.4"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 HAVANA UTR 75662705 75664668 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000321027.8"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-201"; exon_number 17; exon_id "ENSE00003465078.2"; level 2; protein_id "ENSP00000318690.3"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_2"; tag "CCDS"; ccdsid "CCDS1961.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000252255.3"; +chr2 ENSEMBL transcript 75662708 75710985 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75710591 75710985 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 1; exon_id "ENSE00002281229.2"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL CDS 75710591 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 1; exon_id "ENSE00002281229.2"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL start_codon 75710853 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 1; exon_id "ENSE00002281229.2"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75706523 75706651 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 2; exon_id "ENSE00003651464.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL CDS 75706523 75706651 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 2; exon_id "ENSE00003651464.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75702199 75702423 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 3; exon_id "ENSE00003608878.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL CDS 75702199 75702423 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 3; exon_id "ENSE00003608878.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75701190 75701287 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 4; exon_id "ENSE00003668748.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL CDS 75701190 75701287 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 4; exon_id "ENSE00003668748.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75694241 75694427 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 5; exon_id "ENSE00003524832.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL CDS 75694383 75694427 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 5; exon_id "ENSE00003524832.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL stop_codon 75694380 75694382 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 5; exon_id "ENSE00003524832.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75691977 75692100 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 6; exon_id "ENSE00003693895.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75690638 75690719 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 7; exon_id "ENSE00003605616.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75689969 75690081 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 8; exon_id "ENSE00003479763.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75689026 75689225 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 9; exon_id "ENSE00003673268.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75687827 75687977 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 10; exon_id "ENSE00003597384.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75680193 75680314 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 11; exon_id "ENSE00003687660.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75673444 75673520 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 12; exon_id "ENSE00003551346.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75671950 75672016 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 13; exon_id "ENSE00003621594.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75670138 75670284 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 14; exon_id "ENSE00003659152.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75665929 75666053 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 15; exon_id "ENSE00003497772.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL exon 75662708 75664783 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 16; exon_id "ENSE00003721530.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75710856 75710985 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 1; exon_id "ENSE00002281229.2"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75694241 75694382 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 5; exon_id "ENSE00003524832.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75691977 75692100 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 6; exon_id "ENSE00003693895.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75690638 75690719 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 7; exon_id "ENSE00003605616.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75689969 75690081 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 8; exon_id "ENSE00003479763.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75689026 75689225 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 9; exon_id "ENSE00003673268.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75687827 75687977 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 10; exon_id "ENSE00003597384.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75680193 75680314 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 11; exon_id "ENSE00003687660.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75673444 75673520 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 12; exon_id "ENSE00003551346.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75671950 75672016 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 13; exon_id "ENSE00003621594.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75670138 75670284 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 14; exon_id "ENSE00003659152.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75665929 75666053 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 15; exon_id "ENSE00003497772.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 ENSEMBL UTR 75662708 75664783 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000541687.5"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-211"; exon_number 16; exon_id "ENSE00003721530.1"; level 3; protein_id "ENSP00000437767.1"; transcript_support_level "2"; hgnc_id "HGNC:1317"; tag "basic"; havana_gene "OTTHUMG00000129989.5"; +chr2 HAVANA transcript 75664419 75710892 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75710591 75710892 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 1; exon_id "ENSE00001910556.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75710591 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 1; exon_id "ENSE00001910556.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA start_codon 75710853 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 1; exon_id "ENSE00001910556.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75706523 75706651 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 2; exon_id "ENSE00003651464.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75706523 75706651 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 2; exon_id "ENSE00003651464.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75702313 75702423 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 3; exon_id "ENSE00001577517.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75702313 75702423 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 3; exon_id "ENSE00001577517.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75701190 75701287 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 4; exon_id "ENSE00003668748.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75701190 75701287 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 4; exon_id "ENSE00003668748.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75696200 75696315 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 5; exon_id "ENSE00003492242.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75696200 75696315 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 5; exon_id "ENSE00003492242.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75694241 75694427 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 6; exon_id "ENSE00003663933.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75694241 75694427 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 6; exon_id "ENSE00003663933.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75691977 75692100 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 7; exon_id "ENSE00003535454.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75691977 75692100 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 7; exon_id "ENSE00003535454.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75690638 75690719 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 8; exon_id "ENSE00003556420.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75690638 75690719 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 8; exon_id "ENSE00003556420.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75689969 75690081 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 9; exon_id "ENSE00003593081.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75689969 75690081 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 9; exon_id "ENSE00003593081.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75689026 75689225 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 10; exon_id "ENSE00003615519.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75689026 75689225 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 10; exon_id "ENSE00003615519.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75687827 75687977 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 11; exon_id "ENSE00003566359.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75687827 75687977 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 11; exon_id "ENSE00003566359.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75680193 75680314 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 12; exon_id "ENSE00003522865.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75680193 75680314 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 12; exon_id "ENSE00003522865.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75673444 75673520 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 13; exon_id "ENSE00003474620.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75673444 75673520 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 13; exon_id "ENSE00003474620.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75671950 75672016 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 14; exon_id "ENSE00003475605.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75671950 75672016 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 14; exon_id "ENSE00003475605.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75670138 75670284 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 15; exon_id "ENSE00003563051.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75670138 75670284 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 15; exon_id "ENSE00003563051.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75665929 75666053 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 16; exon_id "ENSE00003582023.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75665929 75666053 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 16; exon_id "ENSE00003582023.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA exon 75664419 75664783 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 17; exon_id "ENSE00001837077.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA CDS 75664669 75664783 . - 1 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 17; exon_id "ENSE00001837077.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA stop_codon 75664666 75664668 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 17; exon_id "ENSE00001837077.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA UTR 75710856 75710892 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 1; exon_id "ENSE00001910556.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA UTR 75664419 75664668 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000409857.7"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-202"; exon_number 17; exon_id "ENSE00001837077.1"; level 1; protein_id "ENSP00000386552.3"; transcript_support_level "5"; hgnc_id "HGNC:1317"; tag "basic"; tag "appris_alternative_2"; tag "exp_conf"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328715.1"; +chr2 HAVANA transcript 75701796 75710899 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA exon 75710591 75710899 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 1; exon_id "ENSE00001905495.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA CDS 75710591 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 1; exon_id "ENSE00001905495.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA start_codon 75710853 75710855 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 1; exon_id "ENSE00001905495.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA exon 75706523 75706651 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 2; exon_id "ENSE00003651464.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA CDS 75706523 75706651 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 2; exon_id "ENSE00003651464.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA exon 75701796 75702423 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 3; exon_id "ENSE00001956115.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA CDS 75702173 75702423 . - 2 gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 3; exon_id "ENSE00001956115.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA stop_codon 75702170 75702172 . - 0 gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 3; exon_id "ENSE00001956115.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA UTR 75710856 75710899 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 1; exon_id "ENSE00001905495.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; +chr2 HAVANA UTR 75701796 75702172 . - . gene_id "ENSG00000005436.14"; transcript_id "ENST00000470503.1"; gene_type "protein_coding"; gene_name "GCFC2"; transcript_type "protein_coding"; transcript_name "GCFC2-207"; exon_number 3; exon_id "ENSE00001956115.1"; level 2; protein_id "ENSP00000474481.1"; transcript_support_level "1"; hgnc_id "HGNC:1317"; tag "basic"; tag "CCDS"; ccdsid "CCDS62943.1"; havana_gene "OTTHUMG00000129989.5"; havana_transcript "OTTHUMT00000328714.2"; diff --git a/examples/borzoi_example_eqtl_chr10_116952944_T_C.ipynb b/examples/borzoi_example_eqtl_chr10_116952944_T_C.ipynb index 7e1e2e6..b66c8ae 100644 --- a/examples/borzoi_example_eqtl_chr10_116952944_T_C.ipynb +++ b/examples/borzoi_example_eqtl_chr10_116952944_T_C.ipynb @@ -10,9 +10,12 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 11:08:24.099808: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", + "2024-09-26 17:59:51.449884: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered\n", + "2024-09-26 17:59:51.449959: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered\n", + "2024-09-26 17:59:51.451178: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered\n", + "2024-09-26 17:59:51.459254: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", "To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", - "2023-09-26 11:08:35.392354: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" + "2024-09-26 17:59:53.076138: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" ] } ], @@ -43,28 +46,25 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "id": "a6315e46-79ce-4653-ba71-242e74516b47", "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "bash: /home/jlinder/anaconda3/envs/borzoi_py39_2/lib/libtinfo.so.6: no version information available (required by bash)\n" - ] - }, { "name": "stdout", "output_type": "stream", "text": [ - "f0 model already exists.\n", - "f1 model already exists.\n", - "f2 model already exists.\n", - "f3 model already exists.\n", - "Annotation already exists.\n", - "Splice sites already exist.\n", - "PolyA sites already exist.\n", + "f3c0 model already exists.\n", + "f3c1 model already exists.\n", + "f3c2 model already exists.\n", + "f3c3 model already exists.\n", + "Gene annotation already exists.\n", + "Gene annotation (no read-through, protein-coding) already exists.\n", + "Gene annotation (protein-coding) already exists.\n", + "TSS annotation already exists.\n", + "Splice site annotation already exist.\n", + "Splice site annotation already exist.\n", + "PolyA site annotation already exist.\n", "Human genome FASTA already exists.\n" ] } @@ -72,77 +72,100 @@ "source": [ "%%bash\n", "\n", - "#Download model weights\n", - "for rep in f0 f1 f2 f3; do\n", - " mkdir -p \"saved_models/$rep/\"\n", - " local_model=\"saved_models/$rep/model0_best.h5\"\n", + "#Download model weights (data fold 3, 4 replicates)\n", + "for rep in f3c0,f0 f3c1,f1 f3c2,f2 f3c3,f3; do IFS=\",\"; set -- $rep; \n", + " mkdir -p \"saved_models/$1/train\"\n", + " local_model=\"saved_models/$1/train/model0_best.h5\"\n", " if [ -f \"$local_model\" ]; then\n", - " echo \"$rep model already exists.\"\n", + " echo \"$1 model already exists.\"\n", " else\n", - " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$rep/model0_best.h5\" -O \"$local_model\"\n", + " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$2/model0_best.h5\" -O \"$local_model\"\n", " fi\n", "done\n", "\n", "#Download and uncompress annotation files\n", - "if [ -f gencode41_basic_nort.gtf ]; then\n", - " echo \"Annotation already exists.\"\n", + "mkdir -p hg38/genes/gencode41\n", + "mkdir -p hg38/genes/polyadb\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort.gtf ]; then\n", + " echo \"Gene annotation already exists.\"\n", "else\n", - " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > gencode41_basic_nort.gtf\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort.gtf\n", "fi\n", - "if [ -f gencode41_basic_protein_splice.csv.gz ]; then\n", - " echo \"Splice sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort_protein.gtf ]; then\n", + " echo \"Gene annotation (no read-through, protein-coding) already exists.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort_protein.gtf\n", "fi\n", - "if [ -f polyadb_human_v3.csv.gz ]; then\n", - " echo \"PolyA sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein.gtf ]; then\n", + " echo \"Gene annotation (protein-coding) already exists.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein.gtf\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_tss2.bed ]; then\n", + " echo \"TSS annotation already exists.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_tss2.bed.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_tss2.bed\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz ]; then\n", + " echo \"Splice site annotation already exist.\"\n", + "else\n", + " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz -O hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.gff ]; then\n", + " echo \"Splice site annotation already exist.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.gff.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein_splice.gff\n", + "fi\n", + "\n", + "if [ -f hg38/genes/polyadb/polyadb_human_v3.csv.gz ]; then\n", + " echo \"PolyA site annotation already exist.\"\n", + "else\n", + " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz -O hg38/genes/polyadb/polyadb_human_v3.csv.gz\n", "fi\n", "\n", "#Download and index hg38 genome\n", - "if [ -f hg38.fa ]; then\n", + "mkdir -p hg38/assembly/ucsc\n", + "\n", + "if [ -f hg38/assembly/ucsc/hg38.fa ]; then\n", " echo \"Human genome FASTA already exists.\"\n", "else\n", - " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38.fa\n", - "fi" + " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38/assembly/ucsc/hg38.fa\n", + "fi\n" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 6, "id": "f3dfe8ad-5c40-44b1-aab6-58491694da5d", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "Faidx(\"hg38.fa\")" + "Faidx(\"hg38/assembly/ucsc/hg38.fa\")" ] }, - "execution_count": 3, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "pyfaidx.Faidx('hg38.fa')" + "pyfaidx.Faidx('hg38/assembly/ucsc/hg38.fa')" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 8, "id": "e5fbf3da", "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2023-09-26 11:10:26.366636: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1635] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10372 MB memory: -> device: 0, name: NVIDIA GeForce GTX 1080 Ti, pci bus id: 0000:81:00.0, compute capability: 6.1\n" - ] - } - ], + "outputs": [], "source": [ "#Model configuration\n", "\n", @@ -181,7 +204,7 @@ "models = []\n", "for rep_ix in range(n_reps) :\n", " \n", - " model_file = \"saved_models/f\" + str(rep_ix) + \"/model0_best.h5\"\n", + " model_file = \"saved_models/f3c\" + str(rep_ix) + \"/train/model0_best.h5\"\n", "\n", " seqnn_model = seqnn.SeqNN(params_model)\n", " seqnn_model.restore(model_file, 0)\n", @@ -195,7 +218,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 9, "id": "6f010781", "metadata": { "scrolled": true @@ -212,25 +235,25 @@ "source": [ "#Initialize fasta sequence extractor\n", "\n", - "fasta_open = pysam.Fastafile('hg38.fa')\n", + "fasta_open = pysam.Fastafile('hg38/assembly/ucsc/hg38.fa')\n", "\n", "#Load splice site annotation\n", "\n", - "splice_df = pd.read_csv('gencode41_basic_protein_splice.csv.gz', sep='\\t', compression='gzip')\n", + "splice_df = pd.read_csv('hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz', sep='\\t', compression='gzip')\n", "\n", "print(\"len(splice_df) = \" + str(len(splice_df)))\n" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 10, "id": "12df90e4", "metadata": {}, "outputs": [], "source": [ "#Load GTF (optional; needed to compute exon coverage attributions for example gene)\n", "\n", - "transcriptome = bgene.Transcriptome('gencode41_basic_nort.gtf')\n", + "transcriptome = bgene.Transcriptome('hg38/genes/gencode41/gencode41_basic_nort.gtf')\n", "\n", "search_gene = 'ENSG00000187164'\n", "center_pos = 116952944\n", @@ -256,7 +279,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 11, "id": "073e4711", "metadata": {}, "outputs": [ @@ -280,7 +303,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 12, "id": "4ad40138", "metadata": { "scrolled": true @@ -290,8 +313,9 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 11:12:04.278470: I tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:424] Loaded cuDNN version 8600\n", - "2023-09-26 11:12:20.024423: I tensorflow/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" + "2024-09-25 10:47:49.900745: I external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:454] Loaded cuDNN version 8907\n", + "2024-09-25 10:47:52.112099: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n", + "2024-09-25 10:47:54.815324: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" ] }, { @@ -299,8 +323,8 @@ "output_type": "stream", "text": [ "-- Counts --\n", - " - sum_wt = 134628.16\n", - " - sum_mut = 136860.81\n", + " - sum_wt = 138084.66\n", + " - sum_mut = 140380.31\n", " - max_y_wt = 1051.197\n", " - max_y_mut = 1060.9895\n", " -- (max_y = 1060.9895)\n" @@ -308,7 +332,7 @@ }, { "data": { - "image/png": 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", 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" ] @@ -320,8 +344,8 @@ "name": "stdout", "output_type": "stream", "text": [ - " - sum_wt = 75068.61\n", - " - sum_mut = 90392.24\n", + " - sum_wt = 77193.69\n", + " - sum_mut = 93064.84\n", " - max_y_wt = 696.2884\n", " - max_y_mut = 837.6076\n", " -- (max_y = 837.6076)\n" @@ -329,7 +353,7 @@ }, { "data": { - "image/png": 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" ] @@ -341,8 +365,8 @@ "name": "stdout", "output_type": "stream", "text": [ - " - sum_wt = 44652.867\n", - " - sum_mut = 45602.734\n", + " - sum_wt = 45951.043\n", + " - sum_mut = 46931.766\n", " - max_y_wt = 425.3462\n", " - max_y_mut = 430.3084\n", " -- (max_y = 430.3084)\n" @@ -350,7 +374,7 @@ }, { "data": { - "image/png": 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" ] @@ -362,8 +386,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "CPU times: user 56.5 s, sys: 1.8 s, total: 58.3 s\n", - "Wall time: 1min 28s\n" + "CPU times: user 1min 6s, sys: 941 ms, total: 1min 7s\n", + "Wall time: 1min 18s\n" ] } ], @@ -900,7 +924,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.13" + "version": "3.8.15" } }, "nbformat": 4, diff --git a/examples/borzoi_example_ipaqtl_chr10_116664061_G_A.ipynb b/examples/borzoi_example_ipaqtl_chr10_116664061_G_A.ipynb index 723fdbe..a412d73 100644 --- a/examples/borzoi_example_ipaqtl_chr10_116664061_G_A.ipynb +++ b/examples/borzoi_example_ipaqtl_chr10_116664061_G_A.ipynb @@ -10,9 +10,12 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-27 09:37:40.216505: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", + "2024-09-26 18:00:42.776653: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered\n", + "2024-09-26 18:00:42.776733: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered\n", + "2024-09-26 18:00:42.777952: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered\n", + "2024-09-26 18:00:42.787432: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", "To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", - "2023-09-27 09:37:43.728456: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" + "2024-09-26 18:00:44.230820: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" ] } ], @@ -47,24 +50,21 @@ "id": "a8911e01", "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "bash: /home/jlinder/anaconda3/envs/borzoi_py39_2/lib/libtinfo.so.6: no version information available (required by bash)\n" - ] - }, { "name": "stdout", "output_type": "stream", "text": [ - "f0 model already exists.\n", - "f1 model already exists.\n", - "f2 model already exists.\n", - "f3 model already exists.\n", - "Annotation already exists.\n", - "Splice sites already exist.\n", - "PolyA sites already exist.\n", + "f3c0 model already exists.\n", + "f3c1 model already exists.\n", + "f3c2 model already exists.\n", + "f3c3 model already exists.\n", + "Gene annotation already exists.\n", + "Gene annotation (no read-through, protein-coding) already exists.\n", + "Gene annotation (protein-coding) already exists.\n", + "TSS annotation already exists.\n", + "Splice site annotation already exist.\n", + "Splice site annotation already exist.\n", + "PolyA site annotation already exist.\n", "Human genome FASTA already exists.\n" ] } @@ -72,40 +72,71 @@ "source": [ "%%bash\n", "\n", - "#Download model weights\n", - "for rep in f0 f1 f2 f3; do\n", - " mkdir -p \"saved_models/$rep/\"\n", - " local_model=\"saved_models/$rep/model0_best.h5\"\n", + "#Download model weights (data fold 3, 4 replicates)\n", + "for rep in f3c0,f0 f3c1,f1 f3c2,f2 f3c3,f3; do IFS=\",\"; set -- $rep; \n", + " mkdir -p \"saved_models/$1/train\"\n", + " local_model=\"saved_models/$1/train/model0_best.h5\"\n", " if [ -f \"$local_model\" ]; then\n", - " echo \"$rep model already exists.\"\n", + " echo \"$1 model already exists.\"\n", " else\n", - " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$rep/model0_best.h5\" -O \"$local_model\"\n", + " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$2/model0_best.h5\" -O \"$local_model\"\n", " fi\n", "done\n", "\n", "#Download and uncompress annotation files\n", - "if [ -f gencode41_basic_nort.gtf ]; then\n", - " echo \"Annotation already exists.\"\n", + "mkdir -p hg38/genes/gencode41\n", + "mkdir -p hg38/genes/polyadb\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort.gtf ]; then\n", + " echo \"Gene annotation already exists.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort.gtf\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort_protein.gtf ]; then\n", + " echo \"Gene annotation (no read-through, protein-coding) already exists.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort_protein.gtf\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein.gtf ]; then\n", + " echo \"Gene annotation (protein-coding) already exists.\"\n", "else\n", - " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > gencode41_basic_nort.gtf\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein.gtf\n", "fi\n", - "if [ -f gencode41_basic_protein_splice.csv.gz ]; then\n", - " echo \"Splice sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_tss2.bed ]; then\n", + " echo \"TSS annotation already exists.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_tss2.bed.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_tss2.bed\n", "fi\n", - "if [ -f polyadb_human_v3.csv.gz ]; then\n", - " echo \"PolyA sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz ]; then\n", + " echo \"Splice site annotation already exist.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz\n", + " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz -O hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.gff ]; then\n", + " echo \"Splice site annotation already exist.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.gff.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein_splice.gff\n", + "fi\n", + "\n", + "if [ -f hg38/genes/polyadb/polyadb_human_v3.csv.gz ]; then\n", + " echo \"PolyA site annotation already exist.\"\n", + "else\n", + " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz -O hg38/genes/polyadb/polyadb_human_v3.csv.gz\n", "fi\n", "\n", "#Download and index hg38 genome\n", - "if [ -f hg38.fa ]; then\n", + "mkdir -p hg38/assembly/ucsc\n", + "\n", + "if [ -f hg38/assembly/ucsc/hg38.fa ]; then\n", " echo \"Human genome FASTA already exists.\"\n", "else\n", - " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38.fa\n", - "fi" + " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38/assembly/ucsc/hg38.fa\n", + "fi\n" ] }, { @@ -117,7 +148,7 @@ { "data": { "text/plain": [ - "Faidx(\"hg38.fa\")" + "Faidx(\"hg38/assembly/ucsc/hg38.fa\")" ] }, "execution_count": 3, @@ -126,7 +157,7 @@ } ], "source": [ - "pyfaidx.Faidx('hg38.fa')" + "pyfaidx.Faidx('hg38/assembly/ucsc/hg38.fa')" ] }, { @@ -139,7 +170,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-27 09:38:21.436402: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1635] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10372 MB memory: -> device: 0, name: NVIDIA GeForce GTX 1080 Ti, pci bus id: 0000:81:00.0, compute capability: 6.1\n" + "2024-09-25 11:00:38.644220: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1929] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10232 MB memory: -> device: 0, name: NVIDIA GeForce GTX 1080 Ti, pci bus id: 0000:02:00.0, compute capability: 6.1\n" ] } ], @@ -181,7 +212,7 @@ "models = []\n", "for rep_ix in range(n_reps) :\n", " \n", - " model_file = \"saved_models/f\" + str(rep_ix) + \"/model0_best.h5\"\n", + " model_file = \"saved_models/f3c\" + str(rep_ix) + \"/train/model0_best.h5\"\n", "\n", " seqnn_model = seqnn.SeqNN(params_model)\n", " seqnn_model.restore(model_file, 0)\n", @@ -210,11 +241,11 @@ "source": [ "#Initialize fasta sequence extractor\n", "\n", - "fasta_open = pysam.Fastafile('hg38.fa')\n", + "fasta_open = pysam.Fastafile('hg38/assembly/ucsc/hg38.fa')\n", "\n", "#Load splice site annotation\n", "\n", - "splice_df = pd.read_csv('gencode41_basic_protein_splice.csv.gz', sep='\\t', compression='gzip')\n", + "splice_df = pd.read_csv('hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz', sep='\\t', compression='gzip')\n", "\n", "print(\"len(splice_df) = \" + str(len(splice_df)))\n" ] @@ -255,8 +286,9 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-27 09:39:03.367207: I tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:424] Loaded cuDNN version 8600\n", - "2023-09-27 09:39:03.874328: I tensorflow/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" + "2024-09-25 11:00:55.770144: I external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:454] Loaded cuDNN version 8907\n", + "2024-09-25 11:00:55.859364: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n", + "2024-09-25 11:00:56.180294: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" ] }, { @@ -271,7 +303,7 @@ }, { "data": { - "image/png": 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", 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", 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", 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" ] @@ -321,8 +353,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "CPU times: user 15.1 s, sys: 683 ms, total: 15.8 s\n", - "Wall time: 18.1 s\n" + "CPU times: user 21.5 s, sys: 395 ms, total: 21.9 s\n", + "Wall time: 24.7 s\n" ] } ], @@ -1230,7 +1262,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.13" + "version": "3.8.15" } }, "nbformat": 4, diff --git a/examples/borzoi_example_paqtl_chr1_236763042_A_G.ipynb b/examples/borzoi_example_paqtl_chr1_236763042_A_G.ipynb index bbafdcf..13b5ea0 100644 --- a/examples/borzoi_example_paqtl_chr1_236763042_A_G.ipynb +++ b/examples/borzoi_example_paqtl_chr1_236763042_A_G.ipynb @@ -10,9 +10,12 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 14:38:55.869262: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", + "2024-09-26 18:01:09.612911: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered\n", + "2024-09-26 18:01:09.612989: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered\n", + "2024-09-26 18:01:09.614154: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered\n", + "2024-09-26 18:01:09.622849: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", "To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", - "2023-09-26 14:38:59.736627: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" + "2024-09-26 18:01:11.655064: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" ] } ], @@ -49,24 +52,21 @@ "scrolled": true }, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "bash: /home/jlinder/anaconda3/envs/borzoi_py39_2/lib/libtinfo.so.6: no version information available (required by bash)\n" - ] - }, { "name": "stdout", "output_type": "stream", "text": [ - "f0 model already exists.\n", - "f1 model already exists.\n", - "f2 model already exists.\n", - "f3 model already exists.\n", - "Annotation already exists.\n", - "Splice sites already exist.\n", - "PolyA sites already exist.\n", + "f3c0 model already exists.\n", + "f3c1 model already exists.\n", + "f3c2 model already exists.\n", + "f3c3 model already exists.\n", + "Gene annotation already exists.\n", + "Gene annotation (no read-through, protein-coding) already exists.\n", + "Gene annotation (protein-coding) already exists.\n", + "TSS annotation already exists.\n", + "Splice site annotation already exist.\n", + "Splice site annotation already exist.\n", + "PolyA site annotation already exist.\n", "Human genome FASTA already exists.\n" ] } @@ -74,40 +74,71 @@ "source": [ "%%bash\n", "\n", - "#Download model weights\n", - "for rep in f0 f1 f2 f3; do\n", - " mkdir -p \"saved_models/$rep/\"\n", - " local_model=\"saved_models/$rep/model0_best.h5\"\n", + "#Download model weights (data fold 3, 4 replicates)\n", + "for rep in f3c0,f0 f3c1,f1 f3c2,f2 f3c3,f3; do IFS=\",\"; set -- $rep; \n", + " mkdir -p \"saved_models/$1/train\"\n", + " local_model=\"saved_models/$1/train/model0_best.h5\"\n", " if [ -f \"$local_model\" ]; then\n", - " echo \"$rep model already exists.\"\n", + " echo \"$1 model already exists.\"\n", " else\n", - " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$rep/model0_best.h5\" -O \"$local_model\"\n", + " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$2/model0_best.h5\" -O \"$local_model\"\n", " fi\n", "done\n", "\n", "#Download and uncompress annotation files\n", - "if [ -f gencode41_basic_nort.gtf ]; then\n", - " echo \"Annotation already exists.\"\n", + "mkdir -p hg38/genes/gencode41\n", + "mkdir -p hg38/genes/polyadb\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort.gtf ]; then\n", + " echo \"Gene annotation already exists.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort.gtf\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort_protein.gtf ]; then\n", + " echo \"Gene annotation (no read-through, protein-coding) already exists.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort_protein.gtf\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein.gtf ]; then\n", + " echo \"Gene annotation (protein-coding) already exists.\"\n", "else\n", - " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > gencode41_basic_nort.gtf\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein.gtf\n", "fi\n", - "if [ -f gencode41_basic_protein_splice.csv.gz ]; then\n", - " echo \"Splice sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_tss2.bed ]; then\n", + " echo \"TSS annotation already exists.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_tss2.bed.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_tss2.bed\n", "fi\n", - "if [ -f polyadb_human_v3.csv.gz ]; then\n", - " echo \"PolyA sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz ]; then\n", + " echo \"Splice site annotation already exist.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz\n", + " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz -O hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.gff ]; then\n", + " echo \"Splice site annotation already exist.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.gff.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein_splice.gff\n", + "fi\n", + "\n", + "if [ -f hg38/genes/polyadb/polyadb_human_v3.csv.gz ]; then\n", + " echo \"PolyA site annotation already exist.\"\n", + "else\n", + " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz -O hg38/genes/polyadb/polyadb_human_v3.csv.gz\n", "fi\n", "\n", "#Download and index hg38 genome\n", - "if [ -f hg38.fa ]; then\n", + "mkdir -p hg38/assembly/ucsc\n", + "\n", + "if [ -f hg38/assembly/ucsc/hg38.fa ]; then\n", " echo \"Human genome FASTA already exists.\"\n", "else\n", - " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38.fa\n", - "fi" + " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38/assembly/ucsc/hg38.fa\n", + "fi\n" ] }, { @@ -119,7 +150,7 @@ { "data": { "text/plain": [ - "Faidx(\"hg38.fa\")" + "Faidx(\"hg38/assembly/ucsc/hg38.fa\")" ] }, "execution_count": 3, @@ -128,7 +159,7 @@ } ], "source": [ - "pyfaidx.Faidx('hg38.fa')" + "pyfaidx.Faidx('hg38/assembly/ucsc/hg38.fa')" ] }, { @@ -141,7 +172,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 14:39:51.526063: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1635] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10372 MB memory: -> device: 0, name: NVIDIA GeForce GTX 1080 Ti, pci bus id: 0000:81:00.0, compute capability: 6.1\n" + "2024-09-25 10:56:52.699671: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1929] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10232 MB memory: -> device: 0, name: NVIDIA GeForce GTX 1080 Ti, pci bus id: 0000:02:00.0, compute capability: 6.1\n" ] } ], @@ -183,7 +214,7 @@ "models = []\n", "for rep_ix in range(n_reps) :\n", " \n", - " model_file = \"saved_models/f\" + str(rep_ix) + \"/model0_best.h5\"\n", + " model_file = \"saved_models/f3c\" + str(rep_ix) + \"/train/model0_best.h5\"\n", "\n", " seqnn_model = seqnn.SeqNN(params_model)\n", " seqnn_model.restore(model_file, 0)\n", @@ -214,11 +245,11 @@ "source": [ "#Initialize fasta sequence extractor\n", "\n", - "fasta_open = pysam.Fastafile('hg38.fa')\n", + "fasta_open = pysam.Fastafile('hg38/assembly/ucsc/hg38.fa')\n", "\n", "#Load APA atlas\n", "\n", - "apa_df = pd.read_csv('polyadb_human_v3.csv.gz', sep='\\t', compression='gzip')\n", + "apa_df = pd.read_csv('hg38/genes/polyadb/polyadb_human_v3.csv.gz', sep='\\t', compression='gzip')\n", "apa_df = apa_df[['pas_id', 'gene', 'chrom', 'position_hg38', 'strand', 'site_num', 'num_sites', 'site_type', 'pas_type', 'total_count']]\n", "\n", "apa_df.loc[apa_df['pas_type'] == 'NoPAS', 'pas_type'] = 'No_CSE'\n", @@ -265,8 +296,9 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 14:41:44.072667: I tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:424] Loaded cuDNN version 8600\n", - "2023-09-26 14:41:44.604587: I tensorflow/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" + "2024-09-25 10:57:41.889919: I external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:454] Loaded cuDNN version 8907\n", + "2024-09-25 10:57:41.984645: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n", + "2024-09-25 10:57:42.317045: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" ] }, { @@ -281,7 +313,7 @@ }, { "data": { - "image/png": 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", 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", 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" ] @@ -331,8 +363,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "CPU times: user 13.7 s, sys: 731 ms, total: 14.4 s\n", - "Wall time: 16.8 s\n" + "CPU times: user 20.2 s, sys: 443 ms, total: 20.7 s\n", + "Wall time: 23.5 s\n" ] } ], @@ -991,7 +1023,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.13" + "version": "3.8.15" } }, "nbformat": 4, diff --git a/examples/borzoi_example_sqtl_chr9_135548708_G_C.ipynb b/examples/borzoi_example_sqtl_chr9_135548708_G_C.ipynb index 08badbc..c6ef04b 100644 --- a/examples/borzoi_example_sqtl_chr9_135548708_G_C.ipynb +++ b/examples/borzoi_example_sqtl_chr9_135548708_G_C.ipynb @@ -10,9 +10,12 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 19:11:42.111709: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", + "2024-09-26 18:01:12.492280: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered\n", + "2024-09-26 18:01:12.493991: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered\n", + "2024-09-26 18:01:12.495545: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered\n", + "2024-09-26 18:01:12.508859: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", "To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", - "2023-09-26 19:11:45.658475: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" + "2024-09-26 18:01:14.676533: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n" ] } ], @@ -47,24 +50,21 @@ "id": "a4238bad", "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "bash: /home/jlinder/anaconda3/envs/borzoi_py39_2/lib/libtinfo.so.6: no version information available (required by bash)\n" - ] - }, { "name": "stdout", "output_type": "stream", "text": [ - "f0 model already exists.\n", - "f1 model already exists.\n", - "f2 model already exists.\n", - "f3 model already exists.\n", - "Annotation already exists.\n", - "Splice sites already exist.\n", - "PolyA sites already exist.\n", + "f3c0 model already exists.\n", + "f3c1 model already exists.\n", + "f3c2 model already exists.\n", + "f3c3 model already exists.\n", + "Gene annotation already exists.\n", + "Gene annotation (no read-through, protein-coding) already exists.\n", + "Gene annotation (protein-coding) already exists.\n", + "TSS annotation already exists.\n", + "Splice site annotation already exist.\n", + "Splice site annotation already exist.\n", + "PolyA site annotation already exist.\n", "Human genome FASTA already exists.\n" ] } @@ -72,40 +72,71 @@ "source": [ "%%bash\n", "\n", - "#Download model weights\n", - "for rep in f0 f1 f2 f3; do\n", - " mkdir -p \"saved_models/$rep/\"\n", - " local_model=\"saved_models/$rep/model0_best.h5\"\n", + "#Download model weights (data fold 3, 4 replicates)\n", + "for rep in f3c0,f0 f3c1,f1 f3c2,f2 f3c3,f3; do IFS=\",\"; set -- $rep; \n", + " mkdir -p \"saved_models/$1/train\"\n", + " local_model=\"saved_models/$1/train/model0_best.h5\"\n", " if [ -f \"$local_model\" ]; then\n", - " echo \"$rep model already exists.\"\n", + " echo \"$1 model already exists.\"\n", " else\n", - " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$rep/model0_best.h5\" -O \"$local_model\"\n", + " wget --progress=bar:force \"https://storage.googleapis.com/seqnn-share/borzoi/$2/model0_best.h5\" -O \"$local_model\"\n", " fi\n", "done\n", "\n", "#Download and uncompress annotation files\n", - "if [ -f gencode41_basic_nort.gtf ]; then\n", - " echo \"Annotation already exists.\"\n", + "mkdir -p hg38/genes/gencode41\n", + "mkdir -p hg38/genes/polyadb\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort.gtf ]; then\n", + " echo \"Gene annotation already exists.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort.gtf\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_nort_protein.gtf ]; then\n", + " echo \"Gene annotation (no read-through, protein-coding) already exists.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_nort_protein.gtf\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein.gtf ]; then\n", + " echo \"Gene annotation (protein-coding) already exists.\"\n", "else\n", - " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_nort.gtf.gz | gunzip -c > gencode41_basic_nort.gtf\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein.gtf.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein.gtf\n", "fi\n", - "if [ -f gencode41_basic_protein_splice.csv.gz ]; then\n", - " echo \"Splice sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_tss2.bed ]; then\n", + " echo \"TSS annotation already exists.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_tss2.bed.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_tss2.bed\n", "fi\n", - "if [ -f polyadb_human_v3.csv.gz ]; then\n", - " echo \"PolyA sites already exist.\"\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz ]; then\n", + " echo \"Splice site annotation already exist.\"\n", "else\n", - " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz\n", + " wget https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.csv.gz -O hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz\n", + "fi\n", + "\n", + "if [ -f hg38/genes/gencode41/gencode41_basic_protein_splice.gff ]; then\n", + " echo \"Splice site annotation already exist.\"\n", + "else\n", + " wget -O - https://storage.googleapis.com/seqnn-share/helper/gencode41_basic_protein_splice.gff.gz | gunzip -c > hg38/genes/gencode41/gencode41_basic_protein_splice.gff\n", + "fi\n", + "\n", + "if [ -f hg38/genes/polyadb/polyadb_human_v3.csv.gz ]; then\n", + " echo \"PolyA site annotation already exist.\"\n", + "else\n", + " wget https://storage.googleapis.com/seqnn-share/helper/polyadb_human_v3.csv.gz -O hg38/genes/polyadb/polyadb_human_v3.csv.gz\n", "fi\n", "\n", "#Download and index hg38 genome\n", - "if [ -f hg38.fa ]; then\n", + "mkdir -p hg38/assembly/ucsc\n", + "\n", + "if [ -f hg38/assembly/ucsc/hg38.fa ]; then\n", " echo \"Human genome FASTA already exists.\"\n", "else\n", - " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38.fa\n", - "fi" + " wget -O - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz | gunzip -c > hg38/assembly/ucsc/hg38.fa\n", + "fi\n" ] }, { @@ -117,7 +148,7 @@ { "data": { "text/plain": [ - "Faidx(\"hg38.fa\")" + "Faidx(\"hg38/assembly/ucsc/hg38.fa\")" ] }, "execution_count": 3, @@ -126,7 +157,7 @@ } ], "source": [ - "pyfaidx.Faidx('hg38.fa')" + "pyfaidx.Faidx('hg38/assembly/ucsc/hg38.fa')" ] }, { @@ -139,7 +170,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 19:11:59.651232: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1635] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10372 MB memory: -> device: 0, name: NVIDIA GeForce GTX 1080 Ti, pci bus id: 0000:81:00.0, compute capability: 6.1\n" + "2024-09-25 10:53:57.292179: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1929] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10232 MB memory: -> device: 0, name: NVIDIA GeForce GTX 1080 Ti, pci bus id: 0000:02:00.0, compute capability: 6.1\n" ] } ], @@ -181,7 +212,7 @@ "models = []\n", "for rep_ix in range(n_reps) :\n", " \n", - " model_file = \"saved_models/f\" + str(rep_ix) + \"/model0_best.h5\"\n", + " model_file = \"saved_models/f3c\" + str(rep_ix) + \"/train/model0_best.h5\"\n", "\n", " seqnn_model = seqnn.SeqNN(params_model)\n", " seqnn_model.restore(model_file, 0)\n", @@ -210,11 +241,11 @@ "source": [ "#Initialize fasta sequence extractor\n", "\n", - "fasta_open = pysam.Fastafile('hg38.fa')\n", + "fasta_open = pysam.Fastafile('hg38/assembly/ucsc/hg38.fa')\n", "\n", "#Load splice site annotation\n", "\n", - "splice_df = pd.read_csv('gencode41_basic_protein_splice.csv.gz', sep='\\t', compression='gzip')\n", + "splice_df = pd.read_csv('hg38/genes/gencode41/gencode41_basic_protein_splice.csv.gz', sep='\\t', compression='gzip')\n", "\n", "print(\"len(splice_df) = \" + str(len(splice_df)))\n" ] @@ -253,8 +284,9 @@ "name": "stderr", "output_type": "stream", "text": [ - "2023-09-26 19:13:40.227238: I tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:424] Loaded cuDNN version 8600\n", - "2023-09-26 19:13:40.745579: I tensorflow/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" + "2024-09-25 10:54:21.155675: I external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:454] Loaded cuDNN version 8907\n", + "2024-09-25 10:54:21.243945: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n", + "2024-09-25 10:54:21.567826: I external/local_tsl/tsl/platform/default/subprocess.cc:304] Start cannot spawn child process: No such file or directory\n" ] }, { @@ -269,7 +301,7 @@ }, { "data": { - "image/png": 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", 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"text/plain": [ "
" ] @@ -300,8 +332,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "CPU times: user 13.1 s, sys: 716 ms, total: 13.9 s\n", - "Wall time: 16.3 s\n" + "CPU times: user 19.5 s, sys: 437 ms, total: 20 s\n", + "Wall time: 22.8 s\n" ] } ], @@ -912,7 +944,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.13" + "version": "3.8.15" } }, "nbformat": 4, diff --git a/examples/params.json b/examples/params.json new file mode 100644 index 0000000..4fe232c --- /dev/null +++ b/examples/params.json @@ -0,0 +1,87 @@ +{ + "train": { + "batch_size": 1, + "shuffle_buffer": 256, + "optimizer": "adam", + "learning_rate": 0.00006, + "loss": "poisson_mn", + "total_weight": 0.2, + "warmup_steps": 20000, + "global_clipnorm": 0.15, + "adam_beta1": 0.9, + "adam_beta2": 0.999, + "patience": 30, + "train_epochs_min": 130, + "train_epochs_max": 180 + }, + "model": { + "seq_length": 524288, + "augment_rc": true, + "augment_shift": 3, + "activation": "gelu", + "norm_type": "batch-sync", + "bn_momentum": 0.9, + "kernel_initializer": "lecun_normal", + "l2_scale": 2.0e-8, + "trunk": [ + { + "name": "conv_dna", + "filters": 512, + "kernel_size": 15, + "norm_type": null, + "activation": "linear", + "pool_size": 2 + }, + { + "name": "res_tower", + "filters_init": 608, + "filters_end": 1536, + "divisible_by": 32, + "kernel_size": 5, + "num_convs": 1, + "pool_size": 2, + "repeat": 6 + }, + { + "name": "transformer_tower", + "key_size": 64, + "heads": 8, + "num_position_features": 32, + "dropout": 0.2, + "mha_l2_scale": 1.0e-8, + "l2_scale": 1.0e-8, + "kernel_initializer": "he_normal", + "repeat": 8 + }, + { + "name": "unet_conv", + "kernel_size": 3, + "upsample_conv": true + }, + { + "name": "unet_conv", + "kernel_size": 3, + "upsample_conv": true + }, + { + "name": "Cropping1D", + "cropping": 5120 + }, + { + "name": "conv_nac", + "filters": 1920, + "dropout": 0.1 + } + ], + "head_human": { + "name": "final", + "units": 7611, + "activation": "softplus" + }, + "head_mouse": { + "name": "final", + "units": 2608, + "activation": "softplus" + } + } +} diff --git a/examples/params_pred.json b/examples/params_pred.json index 4811257..5a432dc 100644 --- a/examples/params_pred.json +++ b/examples/params_pred.json @@ -1,45 +1,45 @@ { "train": { "batch_size": 2, - "shuffle_buffer": 256, + "shuffle_buffer": 256, "optimizer": "adam", - "learning_rate": 0.00006, - "loss": "poisson_mn", - "total_weight": 0.2, + "learning_rate": 0.00006, + "loss": "poisson_mn", + "total_weight": 0.2, "warmup_steps": 20000, "global_clipnorm": 0.15, "adam_beta1": 0.9, "adam_beta2": 0.999, "patience": 30, - "train_epochs_min": 130, - "train_epochs_max": 180 + "train_epochs_min": 130, + "train_epochs_max": 180 }, "model": { - "verbose": false, + "verbose": false, "seq_length": 524288, "augment_rc": true, "augment_shift": 3, "activation": "gelu", "norm_type": "batch-sync", "bn_momentum": 0.9, - "kernel_initializer": "lecun_normal", - "l2_scale": 2.0e-8, + "kernel_initializer": "lecun_normal", + "l2_scale": 2.0e-8, "trunk": [ { "name": "conv_dna", "filters": 512, "kernel_size": 15, - "norm_type": null, - "activation": "linear", + "norm_type": null, + "activation": "linear", "pool_size": 2 }, { "name": "res_tower", "filters_init": 608, - "filters_end": 1536, - "divisible_by": 32, + "filters_end": 1536, + "divisible_by": 32, "kernel_size": 5, - "num_convs": 1, + "num_convs": 1, "pool_size": 2, "repeat": 6 }, @@ -49,21 +49,21 @@ "heads": 8, "num_position_features": 32, "dropout": 0.2, - "mha_l2_scale": 1.0e-8, - "l2_scale": 1.0e-8, - "kernel_initializer": "he_normal", - "repeat": 8 + "mha_l2_scale": 1.0e-8, + "l2_scale": 1.0e-8, + "kernel_initializer": "he_normal", + "repeat": 8 + }, + { + "name": "unet_conv", + "kernel_size": 3, + "upsample_conv": true + }, + { + "name": "unet_conv", + "kernel_size": 3, + "upsample_conv": true }, - { - "name": "unet_conv", - "kernel_size": 3, - "upsample_conv": true - }, - { - "name": "unet_conv", - "kernel_size": 3, - "upsample_conv": true - }, { "name": "Cropping1D", "cropping": 16 @@ -74,7 +74,7 @@ "dropout": 0.1 } ], - "head_human": { + "head_human": { "name": "final", "units": 7611, "activation": "softplus" diff --git a/examples/targets_gtex_liver.txt b/examples/targets_gtex_liver.txt new file mode 100644 index 0000000..4740108 --- /dev/null +++ b/examples/targets_gtex_liver.txt @@ -0,0 +1,4 @@ + identifier file clip clip_soft scale sum_stat strand_pair description +7563 GTEX-11EQ9-0526-SM-5A5JZ.1 /home/drk/tillage/datasets/human/rna/recount3/liver/GTEX-11EQ9-0526-SM-5A5JZ.1/coverage.w5 768 384 0.01 sum_sqrt 7563 RNA:liver +7564 GTEX-1QP66-0226-SM-DPRXS.1 /home/drk/tillage/datasets/human/rna/recount3/liver/GTEX-1QP66-0226-SM-DPRXS.1/coverage.w5 768 384 0.01 sum_sqrt 7564 RNA:liver +7565 GTEX-ZYT6-0626-SM-5E45V.1 /home/drk/tillage/datasets/human/rna/recount3/liver/GTEX-ZYT6-0626-SM-5E45V.1/coverage.w5 768 384 0.01 sum_sqrt 7565 RNA:liver diff --git a/examples/targets_mouse.txt b/examples/targets_mouse.txt new file mode 100644 index 0000000..affb228 --- /dev/null +++ b/examples/targets_mouse.txt @@ -0,0 +1,2609 @@ + identifier file clip clip_soft scale sum_stat strand_pair description +0 CNhs10464+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10464/summary/coverage+.w5 768 384 1.0 sum 1 CAGE:placenta, adult pregnant day17 +1 CNhs10464- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10464/summary/coverage-.w5 768 384 1.0 sum 0 CAGE:placenta, adult pregnant day17 +2 CNhs10465+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10465/summary/coverage+.w5 768 384 1.0 sum 3 CAGE:spleen, adult +3 CNhs10465- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10465/summary/coverage-.w5 768 384 1.0 sum 2 CAGE:spleen, adult +4 CNhs10466+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10466/summary/coverage+.w5 768 384 1.0 sum 5 CAGE:liver, adult pregnant day01 +5 CNhs10466- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10466/summary/coverage-.w5 768 384 1.0 sum 4 CAGE:liver, adult pregnant day01 +6 CNhs10467+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10467/summary/coverage+.w5 768 384 1.0 sum 7 CAGE:cecum, adult +7 CNhs10467- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10467/summary/coverage-.w5 768 384 1.0 sum 6 CAGE:cecum, adult +8 CNhs10468+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10468/summary/coverage+.w5 768 384 1.0 sum 9 CAGE:colon, adult +9 CNhs10468- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10468/summary/coverage-.w5 768 384 1.0 sum 8 CAGE:colon, adult +10 CNhs10469+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10469/summary/coverage+.w5 768 384 1.0 sum 11 CAGE:submandibular gland, adult +11 CNhs10469- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10469/summary/coverage-.w5 768 384 1.0 sum 10 CAGE:submandibular gland, adult +12 CNhs10470+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10470/summary/coverage+.w5 768 384 1.0 sum 13 CAGE:prostate, adult +13 CNhs10470- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10470/summary/coverage-.w5 768 384 1.0 sum 12 CAGE:prostate, adult +14 CNhs10471+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10471/summary/coverage+.w5 768 384 1.0 sum 15 CAGE:thymus, adult +15 CNhs10471- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10471/summary/coverage-.w5 768 384 1.0 sum 14 CAGE:thymus, adult +16 CNhs10472+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10472/summary/coverage+.w5 768 384 1.0 sum 17 CAGE:placenta, adult pregnant day10 +17 CNhs10472- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10472/summary/coverage-.w5 768 384 1.0 sum 16 CAGE:placenta, adult pregnant day10 +18 CNhs10473+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10473/summary/coverage+.w5 768 384 1.0 sum 19 CAGE:cortex, adult +19 CNhs10473- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10473/summary/coverage-.w5 768 384 1.0 sum 18 CAGE:cortex, adult +20 CNhs10474+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10474/summary/coverage+.w5 768 384 1.0 sum 21 CAGE:lung, adult +21 CNhs10474- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10474/summary/coverage-.w5 768 384 1.0 sum 20 CAGE:lung, adult +22 CNhs10475+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10475/summary/coverage+.w5 768 384 1.0 sum 23 CAGE:accessory axillary lymph node, adult +23 CNhs10475- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10475/summary/coverage-.w5 768 384 1.0 sum 22 CAGE:accessory axillary lymph node, adult +24 CNhs10476+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10476/summary/coverage+.w5 768 384 1.0 sum 25 CAGE:mammary gland, adult pregnant day19 +25 CNhs10476- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10476/summary/coverage-.w5 768 384 1.0 sum 24 CAGE:mammary gland, adult pregnant day19 +26 CNhs10477+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10477/summary/coverage+.w5 768 384 1.0 sum 27 CAGE:medulla oblongata, adult +27 CNhs10477- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10477/summary/coverage-.w5 768 384 1.0 sum 26 CAGE:medulla oblongata, adult +28 CNhs10478+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10478/summary/coverage+.w5 768 384 1.0 sum 29 CAGE:hippocampus, adult +29 CNhs10478- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10478/summary/coverage-.w5 768 384 1.0 sum 28 CAGE:hippocampus, adult +30 CNhs10480+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10480/summary/coverage+.w5 768 384 1.0 sum 31 CAGE:mammary gland, adult lactating day02 +31 CNhs10480- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10480/summary/coverage-.w5 768 384 1.0 sum 30 CAGE:mammary gland, adult lactating day02 +32 CNhs10481+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10481/summary/coverage+.w5 768 384 1.0 sum 33 CAGE:urinary bladder, adult +33 CNhs10481- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10481/summary/coverage-.w5 768 384 1.0 sum 32 CAGE:urinary bladder, adult +34 CNhs10482+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10482/summary/coverage+.w5 768 384 1.0 sum 35 CAGE:diencephalon, adult +35 CNhs10482- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10482/summary/coverage-.w5 768 384 1.0 sum 34 CAGE:diencephalon, adult +36 CNhs10483+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10483/summary/coverage+.w5 768 384 1.0 sum 37 CAGE:bone (os femoris), adult +37 CNhs10483- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10483/summary/coverage-.w5 768 384 1.0 sum 36 CAGE:bone (os femoris), adult +38 CNhs10484+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10484/summary/coverage+.w5 768 384 1.0 sum 39 CAGE:eyeball, adult +39 CNhs10484- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10484/summary/coverage-.w5 768 384 1.0 sum 38 CAGE:eyeball, adult +40 CNhs10486+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10486/summary/coverage+.w5 768 384 1.0 sum 41 CAGE:pancreas, adult +41 CNhs10486- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10486/summary/coverage-.w5 768 384 1.0 sum 40 CAGE:pancreas, adult +42 CNhs10487+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10487/summary/coverage+.w5 768 384 1.0 sum 43 CAGE:corpus striatum, adult +43 CNhs10487- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10487/summary/coverage-.w5 768 384 1.0 sum 42 CAGE:corpus striatum, adult +44 CNhs10488+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10488/summary/coverage+.w5 768 384 1.0 sum 45 CAGE:amnion, adult pregnant day17.5 +45 CNhs10488- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10488/summary/coverage-.w5 768 384 1.0 sum 44 CAGE:amnion, adult pregnant day17.5 +46 CNhs10489+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10489/summary/coverage+.w5 768 384 1.0 sum 47 CAGE:olfactory brain, adult +47 CNhs10489- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10489/summary/coverage-.w5 768 384 1.0 sum 46 CAGE:olfactory brain, adult +48 CNhs10490+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10490/summary/coverage+.w5 768 384 1.0 sum 49 CAGE:epididymis, adult +49 CNhs10490- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10490/summary/coverage-.w5 768 384 1.0 sum 48 CAGE:epididymis, adult +50 CNhs10491+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10491/summary/coverage+.w5 768 384 1.0 sum 51 CAGE:vesicular gland, adult +51 CNhs10491- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10491/summary/coverage-.w5 768 384 1.0 sum 50 CAGE:vesicular gland, adult +52 CNhs10492+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10492/summary/coverage+.w5 768 384 1.0 sum 53 CAGE:skin, adult +53 CNhs10492- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10492/summary/coverage-.w5 768 384 1.0 sum 52 CAGE:skin, adult +54 CNhs10493+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10493/summary/coverage+.w5 768 384 1.0 sum 55 CAGE:pituitary gland, adult +55 CNhs10493- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10493/summary/coverage-.w5 768 384 1.0 sum 54 CAGE:pituitary gland, adult +56 CNhs10494+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10494/summary/coverage+.w5 768 384 1.0 sum 57 CAGE:cerebellum, adult +57 CNhs10494- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10494/summary/coverage-.w5 768 384 1.0 sum 56 CAGE:cerebellum, adult +58 CNhs10496+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10496/summary/coverage+.w5 768 384 1.0 sum 59 CAGE:intestine, adult +59 CNhs10496- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10496/summary/coverage-.w5 768 384 1.0 sum 58 CAGE:intestine, adult +60 CNhs10497+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10497/summary/coverage+.w5 768 384 1.0 sum 61 CAGE:uterus, adult pregnant day19 +61 CNhs10497- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10497/summary/coverage-.w5 768 384 1.0 sum 60 CAGE:uterus, adult pregnant day19 +62 CNhs10498+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10498/summary/coverage+.w5 768 384 1.0 sum 63 CAGE:aorta, adult +63 CNhs10498- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10498/summary/coverage-.w5 768 384 1.0 sum 62 CAGE:aorta, adult +64 CNhs10499+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10499/summary/coverage+.w5 768 384 1.0 sum 65 CAGE:tongue, adult +65 CNhs10499- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10499/summary/coverage-.w5 768 384 1.0 sum 64 CAGE:tongue, adult +66 CNhs10500+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10500/summary/coverage+.w5 768 384 1.0 sum 67 CAGE:oviduct, adult pregnant day01 +67 CNhs10500- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10500/summary/coverage-.w5 768 384 1.0 sum 66 CAGE:oviduct, adult pregnant day01 +68 CNhs10501+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10501/summary/coverage+.w5 768 384 1.0 sum 69 CAGE:corpora quadrigemina, adult +69 CNhs10501- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10501/summary/coverage-.w5 768 384 1.0 sum 68 CAGE:corpora quadrigemina, adult +70 CNhs10502+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10502/summary/coverage+.w5 768 384 1.0 sum 71 CAGE:vagina, adult +71 CNhs10502- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10502/summary/coverage-.w5 768 384 1.0 sum 70 CAGE:vagina, adult +72 CNhs10503+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10503/summary/coverage+.w5 768 384 1.0 sum 73 CAGE:stomach, adult +73 CNhs10503- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10503/summary/coverage-.w5 768 384 1.0 sum 72 CAGE:stomach, adult +74 CNhs10504+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10504/summary/coverage+.w5 768 384 1.0 sum 75 CAGE:testis, adult +75 CNhs10504- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10504/summary/coverage-.w5 768 384 1.0 sum 74 CAGE:testis, adult +76 CNhs10505+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10505/summary/coverage+.w5 768 384 1.0 sum 77 CAGE:spinal cord, adult +77 CNhs10505- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10505/summary/coverage-.w5 768 384 1.0 sum 76 CAGE:spinal cord, adult +78 CNhs10506+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10506/summary/coverage+.w5 768 384 1.0 sum 79 CAGE:intestinal mucosa, adult +79 CNhs10506- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10506/summary/coverage-.w5 768 384 1.0 sum 78 CAGE:intestinal mucosa, adult +80 CNhs10507+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10507/summary/coverage+.w5 768 384 1.0 sum 81 CAGE:ovary, adult +81 CNhs10507- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10507/summary/coverage-.w5 768 384 1.0 sum 80 CAGE:ovary, adult +82 CNhs10508+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10508/summary/coverage+.w5 768 384 1.0 sum 83 CAGE:adrenal gland, adult +83 CNhs10508- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10508/summary/coverage-.w5 768 384 1.0 sum 82 CAGE:adrenal gland, adult +84 CNhs10509+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10509/summary/coverage+.w5 768 384 1.0 sum 85 CAGE:uterus, adult +85 CNhs10509- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10509/summary/coverage-.w5 768 384 1.0 sum 84 CAGE:uterus, adult +86 CNhs10510+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10510/summary/coverage+.w5 768 384 1.0 sum 87 CAGE:liver, embryo E17 +87 CNhs10510- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10510/summary/coverage-.w5 768 384 1.0 sum 86 CAGE:liver, embryo E17 +88 CNhs10512+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10512/summary/coverage+.w5 768 384 1.0 sum 89 CAGE:whole body, embryo E13 +89 CNhs10512- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10512/summary/coverage-.w5 768 384 1.0 sum 88 CAGE:whole body, embryo E13 +90 CNhs10513+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10513/summary/coverage+.w5 768 384 1.0 sum 91 CAGE:whole body, embryo E17.5 +91 CNhs10513- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10513/summary/coverage-.w5 768 384 1.0 sum 90 CAGE:whole body, embryo E17.5 +92 CNhs10514+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10514/summary/coverage+.w5 768 384 1.0 sum 93 CAGE:whole body, embryo E16 +93 CNhs10514- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10514/summary/coverage-.w5 768 384 1.0 sum 92 CAGE:whole body, embryo E16 +94 CNhs10515+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10515/summary/coverage+.w5 768 384 1.0 sum 95 CAGE:whole body, neonate N06 +95 CNhs10515- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10515/summary/coverage-.w5 768 384 1.0 sum 94 CAGE:whole body, neonate N06 +96 CNhs10516+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10516/summary/coverage+.w5 768 384 1.0 sum 97 CAGE:whole body, embryo E18 +97 CNhs10516- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10516/summary/coverage-.w5 768 384 1.0 sum 96 CAGE:whole body, embryo E18 +98 CNhs10517+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10517/summary/coverage+.w5 768 384 1.0 sum 99 CAGE:whole body, embryo E17 +99 CNhs10517- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10517/summary/coverage-.w5 768 384 1.0 sum 98 CAGE:whole body, embryo E17 +100 CNhs10518+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10518/summary/coverage+.w5 768 384 1.0 sum 101 CAGE:whole body, neonate N10 +101 CNhs10518- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10518/summary/coverage-.w5 768 384 1.0 sum 100 CAGE:whole body, neonate N10 +102 CNhs10519+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10519/summary/coverage+.w5 768 384 1.0 sum 103 CAGE:whole body, embryo E14 +103 CNhs10519- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10519/summary/coverage-.w5 768 384 1.0 sum 102 CAGE:whole body, embryo E14 +104 CNhs10520+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10520/summary/coverage+.w5 768 384 1.0 sum 105 CAGE:liver, embryo E15 +105 CNhs10520- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10520/summary/coverage-.w5 768 384 1.0 sum 104 CAGE:liver, embryo E15 +106 CNhs10521+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10521/summary/coverage+.w5 768 384 1.0 sum 107 CAGE:eyeball, embryo E14 +107 CNhs10521- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10521/summary/coverage-.w5 768 384 1.0 sum 106 CAGE:eyeball, embryo E14 +108 CNhs10522+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10522/summary/coverage+.w5 768 384 1.0 sum 109 CAGE:lung, embryo E12 +109 CNhs10522- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10522/summary/coverage-.w5 768 384 1.0 sum 108 CAGE:lung, embryo E12 +110 CNhs10523+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10523/summary/coverage+.w5 768 384 1.0 sum 111 CAGE:liver, embryo E16 +111 CNhs10523- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10523/summary/coverage-.w5 768 384 1.0 sum 110 CAGE:liver, embryo E16 +112 CNhs10524+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10524/summary/coverage+.w5 768 384 1.0 sum 113 CAGE:liver, embryo E13 +113 CNhs10524- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10524/summary/coverage-.w5 768 384 1.0 sum 112 CAGE:liver, embryo E13 +114 CNhs10525+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10525/summary/coverage+.w5 768 384 1.0 sum 115 CAGE:whole body, neonate N00 +115 CNhs10525- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10525/summary/coverage-.w5 768 384 1.0 sum 114 CAGE:whole body, neonate N00 +116 CNhs10526+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10526/summary/coverage+.w5 768 384 1.0 sum 117 CAGE:intestine, embryo E18 +117 CNhs10526- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10526/summary/coverage-.w5 768 384 1.0 sum 116 CAGE:intestine, embryo E18 +118 CNhs10576+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10576/summary/coverage+.w5 768 384 1.0 sum 119 CAGE:whole body, neonate N01 +119 CNhs10576- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10576/summary/coverage-.w5 768 384 1.0 sum 118 CAGE:whole body, neonate N01 +120 CNhs10577+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10577/summary/coverage+.w5 768 384 1.0 sum 121 CAGE:forelimb, embryo E14 +121 CNhs10577- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10577/summary/coverage-.w5 768 384 1.0 sum 120 CAGE:forelimb, embryo E14 +122 CNhs10578+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10578/summary/coverage+.w5 768 384 1.0 sum 123 CAGE:whole body, embryo E14.5 +123 CNhs10578- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10578/summary/coverage-.w5 768 384 1.0 sum 122 CAGE:whole body, embryo E14.5 +124 CNhs10579+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10579/summary/coverage+.w5 768 384 1.0 sum 125 CAGE:liver, embryo E18 +125 CNhs10579- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10579/summary/coverage-.w5 768 384 1.0 sum 124 CAGE:liver, embryo E18 +126 CNhs10580+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10580/summary/coverage+.w5 768 384 1.0 sum 127 CAGE:pancreas, embryo E18 +127 CNhs10580- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10580/summary/coverage-.w5 768 384 1.0 sum 126 CAGE:pancreas, embryo E18 +128 CNhs10581+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10581/summary/coverage+.w5 768 384 1.0 sum 129 CAGE:thymus, embryo E17 +129 CNhs10581- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10581/summary/coverage-.w5 768 384 1.0 sum 128 CAGE:thymus, embryo E17 +130 CNhs10582+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10582/summary/coverage+.w5 768 384 1.0 sum 131 CAGE:intestine, embryo E17 +131 CNhs10582- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10582/summary/coverage-.w5 768 384 1.0 sum 130 CAGE:intestine, embryo E17 +132 CNhs10583+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10583/summary/coverage+.w5 768 384 1.0 sum 133 CAGE:lung, embryo E18 +133 CNhs10583- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10583/summary/coverage-.w5 768 384 1.0 sum 132 CAGE:lung, embryo E18 +134 CNhs10584+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10584/summary/coverage+.w5 768 384 1.0 sum 135 CAGE:kidney, embryo E16 +135 CNhs10584- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10584/summary/coverage-.w5 768 384 1.0 sum 134 CAGE:kidney, embryo E16 +136 CNhs10585+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10585/summary/coverage+.w5 768 384 1.0 sum 137 CAGE:intestine, embryo E16 +137 CNhs10585- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10585/summary/coverage-.w5 768 384 1.0 sum 136 CAGE:intestine, embryo E16 +138 CNhs10586+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10586/summary/coverage+.w5 768 384 1.0 sum 139 CAGE:heart, embryo E11 +139 CNhs10586- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10586/summary/coverage-.w5 768 384 1.0 sum 138 CAGE:heart, embryo E11 +140 CNhs10587+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10587/summary/coverage+.w5 768 384 1.0 sum 141 CAGE:whole body, embryo E12 +141 CNhs10587- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10587/summary/coverage-.w5 768 384 1.0 sum 140 CAGE:whole body, embryo E12 +142 CNhs10588+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10588/summary/coverage+.w5 768 384 1.0 sum 143 CAGE:stomach, embryo E12 +143 CNhs10588- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10588/summary/coverage-.w5 768 384 1.0 sum 142 CAGE:stomach, embryo E12 +144 CNhs10589+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10589/summary/coverage+.w5 768 384 1.0 sum 145 CAGE:forelimb, embryo E13 +145 CNhs10589- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10589/summary/coverage-.w5 768 384 1.0 sum 144 CAGE:forelimb, embryo E13 +146 CNhs10592+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10592/summary/coverage+.w5 768 384 1.0 sum 147 CAGE:pituitary gland, embryo E15 +147 CNhs10592- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10592/summary/coverage-.w5 768 384 1.0 sum 146 CAGE:pituitary gland, embryo E15 +148 CNhs10593+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10593/summary/coverage+.w5 768 384 1.0 sum 149 CAGE:eyeball, embryo E15 +149 CNhs10593- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10593/summary/coverage-.w5 768 384 1.0 sum 148 CAGE:eyeball, embryo E15 +150 CNhs10594+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10594/summary/coverage+.w5 768 384 1.0 sum 151 CAGE:liver, embryo E14 +151 CNhs10594- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10594/summary/coverage-.w5 768 384 1.0 sum 150 CAGE:liver, embryo E14 +152 CNhs10595+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10595/summary/coverage+.w5 768 384 1.0 sum 153 CAGE:thymus, embryo E18 +153 CNhs10595- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10595/summary/coverage-.w5 768 384 1.0 sum 152 CAGE:thymus, embryo E18 +154 CNhs10596+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10596/summary/coverage+.w5 768 384 1.0 sum 155 CAGE:forelimb, embryo E11 +155 CNhs10596- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10596/summary/coverage-.w5 768 384 1.0 sum 154 CAGE:forelimb, embryo E11 +156 CNhs10597+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10597/summary/coverage+.w5 768 384 1.0 sum 157 CAGE:heart, embryo E14 +157 CNhs10597- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10597/summary/coverage-.w5 768 384 1.0 sum 156 CAGE:heart, embryo E14 +158 CNhs10598+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10598/summary/coverage+.w5 768 384 1.0 sum 159 CAGE:forelimb, embryo E17 +159 CNhs10598- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10598/summary/coverage-.w5 768 384 1.0 sum 158 CAGE:forelimb, embryo E17 +160 CNhs10599+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10599/summary/coverage+.w5 768 384 1.0 sum 161 CAGE:pancreas, embryo E17 +161 CNhs10599- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10599/summary/coverage-.w5 768 384 1.0 sum 160 CAGE:pancreas, embryo E17 +162 CNhs10600+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10600/summary/coverage+.w5 768 384 1.0 sum 163 CAGE:forelimb, embryo E12 +163 CNhs10600- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10600/summary/coverage-.w5 768 384 1.0 sum 162 CAGE:forelimb, embryo E12 +164 CNhs10601+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10601/summary/coverage+.w5 768 384 1.0 sum 165 CAGE:liver, embryo E12 +165 CNhs10601- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10601/summary/coverage-.w5 768 384 1.0 sum 164 CAGE:liver, embryo E12 +166 CNhs10602+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10602/summary/coverage+.w5 768 384 1.0 sum 167 CAGE:intestine, embryo E15 +167 CNhs10602- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10602/summary/coverage-.w5 768 384 1.0 sum 166 CAGE:intestine, embryo E15 +168 CNhs10603+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10603/summary/coverage+.w5 768 384 1.0 sum 169 CAGE:stomach, embryo E15 +169 CNhs10603- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10603/summary/coverage-.w5 768 384 1.0 sum 168 CAGE:stomach, embryo E15 +170 CNhs10604+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10604/summary/coverage+.w5 768 384 1.0 sum 171 CAGE:lung, embryo E14 +171 CNhs10604- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10604/summary/coverage-.w5 768 384 1.0 sum 170 CAGE:lung, embryo E14 +172 CNhs10605+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10605/summary/coverage+.w5 768 384 1.0 sum 173 CAGE:lung, embryo E17 +173 CNhs10605- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10605/summary/coverage-.w5 768 384 1.0 sum 172 CAGE:lung, embryo E17 +174 CNhs10606+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10606/summary/coverage+.w5 768 384 1.0 sum 175 CAGE:kidney, embryo E14 +175 CNhs10606- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10606/summary/coverage-.w5 768 384 1.0 sum 174 CAGE:kidney, embryo E14 +176 CNhs10609+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10609/summary/coverage+.w5 768 384 1.0 sum 177 CAGE:Clontech Mouse Universal Reference Total RNA, pool1 +177 CNhs10609- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10609/summary/coverage-.w5 768 384 1.0 sum 176 CAGE:Clontech Mouse Universal Reference Total RNA, pool1 +178 CNhs10611+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10611/summary/coverage+.w5 768 384 1.0 sum 179 CAGE:SABiosciences XpressRef Mouse Universal Total RNA, pool1 +179 CNhs10611- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10611/summary/coverage-.w5 768 384 1.0 sum 178 CAGE:SABiosciences XpressRef Mouse Universal Total RNA, pool1 +180 CNhs10613+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10613/summary/coverage+.w5 768 384 1.0 sum 181 CAGE:Universal RNA - Mouse Normal Tissues Biochain, pool1 +181 CNhs10613- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10613/summary/coverage-.w5 768 384 1.0 sum 180 CAGE:Universal RNA - Mouse Normal Tissues Biochain, pool1 +182 CNhs10997+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10997/summary/coverage+.w5 768 384 1.0 sum 183 CAGE:kidney, embryo E15 +183 CNhs10997- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10997/summary/coverage-.w5 768 384 1.0 sum 182 CAGE:kidney, embryo E15 +184 CNhs10998+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10998/summary/coverage+.w5 768 384 1.0 sum 185 CAGE:lung, embryo E16 +185 CNhs10998- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10998/summary/coverage-.w5 768 384 1.0 sum 184 CAGE:lung, embryo E16 +186 CNhs10999+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10999/summary/coverage+.w5 768 384 1.0 sum 187 CAGE:stomach, embryo E18 +187 CNhs10999- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs10999/summary/coverage-.w5 768 384 1.0 sum 186 CAGE:stomach, embryo E18 +188 CNhs11001+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11001/summary/coverage+.w5 768 384 1.0 sum 189 CAGE:kidney, embryo E18 +189 CNhs11001- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11001/summary/coverage-.w5 768 384 1.0 sum 188 CAGE:kidney, embryo E18 +190 CNhs11002+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11002/summary/coverage+.w5 768 384 1.0 sum 191 CAGE:thymus, embryo E16 +191 CNhs11002- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11002/summary/coverage-.w5 768 384 1.0 sum 190 CAGE:thymus, embryo E16 +192 CNhs11003+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11003/summary/coverage+.w5 768 384 1.0 sum 193 CAGE:pancreas, embryo E16 +193 CNhs11003- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11003/summary/coverage-.w5 768 384 1.0 sum 192 CAGE:pancreas, embryo E16 +194 CNhs11004+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11004/summary/coverage+.w5 768 384 1.0 sum 195 CAGE:adrenal gland, embryo E16 +195 CNhs11004- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11004/summary/coverage-.w5 768 384 1.0 sum 194 CAGE:adrenal gland, embryo E16 +196 CNhs11005+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11005/summary/coverage+.w5 768 384 1.0 sum 197 CAGE:thymus, embryo E15 +197 CNhs11005- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11005/summary/coverage-.w5 768 384 1.0 sum 196 CAGE:thymus, embryo E15 +198 CNhs11006+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11006/summary/coverage+.w5 768 384 1.0 sum 199 CAGE:stomach, embryo E17 +199 CNhs11006- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11006/summary/coverage-.w5 768 384 1.0 sum 198 CAGE:stomach, embryo E17 +200 CNhs11007+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11007/summary/coverage+.w5 768 384 1.0 sum 201 CAGE:forelimb, embryo E15 +201 CNhs11007- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11007/summary/coverage-.w5 768 384 1.0 sum 200 CAGE:forelimb, embryo E15 +202 CNhs11008+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11008/summary/coverage+.w5 768 384 1.0 sum 203 CAGE:forelimb, embryo E18 +203 CNhs11008- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11008/summary/coverage-.w5 768 384 1.0 sum 202 CAGE:forelimb, embryo E18 +204 CNhs11009+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11009/summary/coverage+.w5 768 384 1.0 sum 205 CAGE:pituitary gland, embryo E13 +205 CNhs11009- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11009/summary/coverage-.w5 768 384 1.0 sum 204 CAGE:pituitary gland, embryo E13 +206 CNhs11010+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11010/summary/coverage+.w5 768 384 1.0 sum 207 CAGE:intestine, embryo E13 +207 CNhs11010- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11010/summary/coverage-.w5 768 384 1.0 sum 206 CAGE:intestine, embryo E13 +208 CNhs11011+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11011/summary/coverage+.w5 768 384 1.0 sum 209 CAGE:spleen, embryo E18 +209 CNhs11011- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11011/summary/coverage-.w5 768 384 1.0 sum 208 CAGE:spleen, embryo E18 +210 CNhs11012+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11012/summary/coverage+.w5 768 384 1.0 sum 211 CAGE:pancreas, embryo E14 +211 CNhs11012- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11012/summary/coverage-.w5 768 384 1.0 sum 210 CAGE:pancreas, embryo E14 +212 CNhs11013+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11013/summary/coverage+.w5 768 384 1.0 sum 213 CAGE:heart, embryo E13 +213 CNhs11013- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11013/summary/coverage-.w5 768 384 1.0 sum 212 CAGE:heart, embryo E13 +214 CNhs11014+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11014/summary/coverage+.w5 768 384 1.0 sum 215 CAGE:whole body, embryo E11 +215 CNhs11014- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11014/summary/coverage-.w5 768 384 1.0 sum 214 CAGE:whole body, embryo E11 +216 CNhs11015+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11015/summary/coverage+.w5 768 384 1.0 sum 217 CAGE:heart, embryo E12 +217 CNhs11015- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11015/summary/coverage-.w5 768 384 1.0 sum 216 CAGE:heart, embryo E12 +218 CNhs11016+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11016/summary/coverage+.w5 768 384 1.0 sum 219 CAGE:eyeball, embryo E12 +219 CNhs11016- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11016/summary/coverage-.w5 768 384 1.0 sum 218 CAGE:eyeball, embryo E12 +220 CNhs11017+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11017/summary/coverage+.w5 768 384 1.0 sum 221 CAGE:heart, embryo E15 +221 CNhs11017- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11017/summary/coverage-.w5 768 384 1.0 sum 220 CAGE:heart, embryo E15 +222 CNhs11018+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11018/summary/coverage+.w5 768 384 1.0 sum 223 CAGE:pituitary gland, embryo E12 +223 CNhs11018- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11018/summary/coverage-.w5 768 384 1.0 sum 222 CAGE:pituitary gland, embryo E12 +224 CNhs11019+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11019/summary/coverage+.w5 768 384 1.0 sum 225 CAGE:intestine, embryo E12 +225 CNhs11019- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11019/summary/coverage-.w5 768 384 1.0 sum 224 CAGE:intestine, embryo E12 +226 CNhs11020+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11020/summary/coverage+.w5 768 384 1.0 sum 227 CAGE:lung, embryo E15 +227 CNhs11020- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11020/summary/coverage-.w5 768 384 1.0 sum 226 CAGE:lung, embryo E15 +228 CNhs11021+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11021/summary/coverage+.w5 768 384 1.0 sum 229 CAGE:heart, embryo E16 +229 CNhs11021- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11021/summary/coverage-.w5 768 384 1.0 sum 228 CAGE:heart, embryo E16 +230 CNhs11022+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11022/summary/coverage+.w5 768 384 1.0 sum 231 CAGE:stomach, embryo E16 +231 CNhs11022- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11022/summary/coverage-.w5 768 384 1.0 sum 230 CAGE:stomach, embryo E16 +232 CNhs11023+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11023/summary/coverage+.w5 768 384 1.0 sum 233 CAGE:eyeball, embryo E17 +233 CNhs11023- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11023/summary/coverage-.w5 768 384 1.0 sum 232 CAGE:eyeball, embryo E17 +234 CNhs11025+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11025/summary/coverage+.w5 768 384 1.0 sum 235 CAGE:heart, embryo E17 +235 CNhs11025- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11025/summary/coverage-.w5 768 384 1.0 sum 234 CAGE:heart, embryo E17 +236 CNhs11026+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11026/summary/coverage+.w5 768 384 1.0 sum 237 CAGE:adrenal gland, embryo E18 +237 CNhs11026- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11026/summary/coverage-.w5 768 384 1.0 sum 236 CAGE:adrenal gland, embryo E18 +238 CNhs11027+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11027/summary/coverage+.w5 768 384 1.0 sum 239 CAGE:testis, embryo E18 +239 CNhs11027- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11027/summary/coverage-.w5 768 384 1.0 sum 238 CAGE:testis, embryo E18 +240 CNhs11028+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11028/summary/coverage+.w5 768 384 1.0 sum 241 CAGE:kidney, embryo E17 +241 CNhs11028- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11028/summary/coverage-.w5 768 384 1.0 sum 240 CAGE:kidney, embryo E17 +242 CNhs11029+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11029/summary/coverage+.w5 768 384 1.0 sum 243 CAGE:testis, embryo E17 +243 CNhs11029- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11029/summary/coverage-.w5 768 384 1.0 sum 242 CAGE:testis, embryo E17 +244 CNhs11030+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11030/summary/coverage+.w5 768 384 1.0 sum 245 CAGE:heart, embryo E18 +245 CNhs11030- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11030/summary/coverage-.w5 768 384 1.0 sum 244 CAGE:heart, embryo E18 +246 CNhs11031+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11031/summary/coverage+.w5 768 384 1.0 sum 247 CAGE:testis, embryo E13 +247 CNhs11031- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11031/summary/coverage-.w5 768 384 1.0 sum 246 CAGE:testis, embryo E13 +248 CNhs11033+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11033/summary/coverage+.w5 768 384 1.0 sum 249 CAGE:testis, embryo E16 +249 CNhs11033- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11033/summary/coverage-.w5 768 384 1.0 sum 248 CAGE:testis, embryo E16 +250 CNhs11034+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11034/summary/coverage+.w5 768 384 1.0 sum 251 CAGE:testis, embryo E15 +251 CNhs11034- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11034/summary/coverage-.w5 768 384 1.0 sum 250 CAGE:testis, embryo E15 +252 CNhs11035+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11035/summary/coverage+.w5 768 384 1.0 sum 253 CAGE:spleen, embryo E16 +253 CNhs11035- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11035/summary/coverage-.w5 768 384 1.0 sum 252 CAGE:spleen, embryo E16 +254 CNhs11036+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11036/summary/coverage+.w5 768 384 1.0 sum 255 CAGE:pituitary gland, embryo E16 +255 CNhs11036- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11036/summary/coverage-.w5 768 384 1.0 sum 254 CAGE:pituitary gland, embryo E16 +256 CNhs11037+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11037/summary/coverage+.w5 768 384 1.0 sum 257 CAGE:pituitary gland, embryo E14 +257 CNhs11037- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11037/summary/coverage-.w5 768 384 1.0 sum 256 CAGE:pituitary gland, embryo E14 +258 CNhs11038+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11038/summary/coverage+.w5 768 384 1.0 sum 259 CAGE:adrenal gland, embryo E14 +259 CNhs11038- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11038/summary/coverage-.w5 768 384 1.0 sum 258 CAGE:adrenal gland, embryo E14 +260 CNhs11039+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11039/summary/coverage+.w5 768 384 1.0 sum 261 CAGE:pituitary gland, embryo E17 +261 CNhs11039- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11039/summary/coverage-.w5 768 384 1.0 sum 260 CAGE:pituitary gland, embryo E17 +262 CNhs11040+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11040/summary/coverage+.w5 768 384 1.0 sum 263 CAGE:ovary, embryo E18 +263 CNhs11040- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11040/summary/coverage-.w5 768 384 1.0 sum 262 CAGE:ovary, embryo E18 +264 CNhs11041+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11041/summary/coverage+.w5 768 384 1.0 sum 265 CAGE:thymus, embryo E14 +265 CNhs11041- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11041/summary/coverage-.w5 768 384 1.0 sum 264 CAGE:thymus, embryo E14 +266 CNhs11042+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11042/summary/coverage+.w5 768 384 1.0 sum 267 CAGE:pancreas, embryo E15 +267 CNhs11042- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11042/summary/coverage-.w5 768 384 1.0 sum 266 CAGE:pancreas, embryo E15 +268 CNhs11043+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11043/summary/coverage+.w5 768 384 1.0 sum 269 CAGE:adrenal gland, embryo E17 +269 CNhs11043- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11043/summary/coverage-.w5 768 384 1.0 sum 268 CAGE:adrenal gland, embryo E17 +270 CNhs11044+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11044/summary/coverage+.w5 768 384 1.0 sum 271 CAGE:gonad, embryo E13 +271 CNhs11044- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11044/summary/coverage-.w5 768 384 1.0 sum 270 CAGE:gonad, embryo E13 +272 CNhs11056+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11055/summary/coverage+.w5 768 384 1.0 sum 273 CAGE:Mouse Aortic Smooth Muscle cells - differentiated, biol_ +273 CNhs11056- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11055/summary/coverage-.w5 768 384 1.0 sum 272 CAGE:Mouse Aortic Smooth Muscle cells - differentiated, biol_ +274 CNhs11093+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11093/summary/coverage+.w5 768 384 1.0 sum 275 CAGE:mouse fibroblast cell line: CRL-1658 NIH/3T3 +275 CNhs11093- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11093/summary/coverage-.w5 768 384 1.0 sum 274 CAGE:mouse fibroblast cell line: CRL-1658 NIH/3T3 +276 CNhs11094+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11094/summary/coverage+.w5 768 384 1.0 sum 277 CAGE:pancreas, neonate N25 +277 CNhs11094- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11094/summary/coverage-.w5 768 384 1.0 sum 276 CAGE:pancreas, neonate N25 +278 CNhs11095+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11095/summary/coverage+.w5 768 384 1.0 sum 279 CAGE:intestine, neonate N07 +279 CNhs11095- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11095/summary/coverage-.w5 768 384 1.0 sum 278 CAGE:intestine, neonate N07 +280 CNhs11097+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11097/summary/coverage+.w5 768 384 1.0 sum 281 CAGE:skin, neonate N06 +281 CNhs11097- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11097/summary/coverage-.w5 768 384 1.0 sum 280 CAGE:skin, neonate N06 +282 CNhs11098+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11098/summary/coverage+.w5 768 384 1.0 sum 283 CAGE:intestine, neonate N10 +283 CNhs11098- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11098/summary/coverage-.w5 768 384 1.0 sum 282 CAGE:intestine, neonate N10 +284 CNhs11099+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11099/summary/coverage+.w5 768 384 1.0 sum 285 CAGE:spleen, neonate N25 +285 CNhs11099- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11099/summary/coverage-.w5 768 384 1.0 sum 284 CAGE:spleen, neonate N25 +286 CNhs11101+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11101/summary/coverage+.w5 768 384 1.0 sum 287 CAGE:liver, neonate N06 +287 CNhs11101- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11101/summary/coverage-.w5 768 384 1.0 sum 286 CAGE:liver, neonate N06 +288 CNhs11102+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11102/summary/coverage+.w5 768 384 1.0 sum 289 CAGE:intestine, neonate N06 +289 CNhs11102- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11102/summary/coverage-.w5 768 384 1.0 sum 288 CAGE:intestine, neonate N06 +290 CNhs11103+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11103/summary/coverage+.w5 768 384 1.0 sum 291 CAGE:liver, neonate N07 +291 CNhs11103- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11103/summary/coverage-.w5 768 384 1.0 sum 290 CAGE:liver, neonate N07 +292 CNhs11104+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11104/summary/coverage+.w5 768 384 1.0 sum 293 CAGE:stomach, neonate N25 +293 CNhs11104- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11104/summary/coverage-.w5 768 384 1.0 sum 292 CAGE:stomach, neonate N25 +294 CNhs11105+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11105/summary/coverage+.w5 768 384 1.0 sum 295 CAGE:pancreas, neonate N00 +295 CNhs11105- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11105/summary/coverage-.w5 768 384 1.0 sum 294 CAGE:pancreas, neonate N00 +296 CNhs11106+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11106/summary/coverage+.w5 768 384 1.0 sum 297 CAGE:liver, neonate N30 +297 CNhs11106- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11106/summary/coverage-.w5 768 384 1.0 sum 296 CAGE:liver, neonate N30 +298 CNhs11107+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11107/summary/coverage+.w5 768 384 1.0 sum 299 CAGE:cortex, neonate N30 +299 CNhs11107- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11107/summary/coverage-.w5 768 384 1.0 sum 298 CAGE:cortex, neonate N30 +300 CNhs11108+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11108/summary/coverage+.w5 768 384 1.0 sum 301 CAGE:skin, neonate N10 +301 CNhs11108- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11108/summary/coverage-.w5 768 384 1.0 sum 300 CAGE:skin, neonate N10 +302 CNhs11109+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11109/summary/coverage+.w5 768 384 1.0 sum 303 CAGE:lung, neonate N20 +303 CNhs11109- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11109/summary/coverage-.w5 768 384 1.0 sum 302 CAGE:lung, neonate N20 +304 CNhs11110+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11110/summary/coverage+.w5 768 384 1.0 sum 305 CAGE:testis, neonate N20 +305 CNhs11110- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11110/summary/coverage-.w5 768 384 1.0 sum 304 CAGE:testis, neonate N20 +306 CNhs11111+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11111/summary/coverage+.w5 768 384 1.0 sum 307 CAGE:lung, neonate N07 +307 CNhs11111- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11111/summary/coverage-.w5 768 384 1.0 sum 306 CAGE:lung, neonate N07 +308 CNhs11112+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11112/summary/coverage+.w5 768 384 1.0 sum 309 CAGE:spleen, neonate N20 +309 CNhs11112- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11112/summary/coverage-.w5 768 384 1.0 sum 308 CAGE:spleen, neonate N20 +310 CNhs11113+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11113/summary/coverage+.w5 768 384 1.0 sum 311 CAGE:kidney, neonate N20 +311 CNhs11113- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11113/summary/coverage-.w5 768 384 1.0 sum 310 CAGE:kidney, neonate N20 +312 CNhs11114+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11114/summary/coverage+.w5 768 384 1.0 sum 313 CAGE:small intestine, neonate N16 +313 CNhs11114- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11114/summary/coverage-.w5 768 384 1.0 sum 312 CAGE:small intestine, neonate N16 +314 CNhs11115+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11115/summary/coverage+.w5 768 384 1.0 sum 315 CAGE:liver, neonate N10 +315 CNhs11115- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11115/summary/coverage-.w5 768 384 1.0 sum 314 CAGE:liver, neonate N10 +316 CNhs11116+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11116/summary/coverage+.w5 768 384 1.0 sum 317 CAGE:spleen, neonate N10 +317 CNhs11116- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11116/summary/coverage-.w5 768 384 1.0 sum 316 CAGE:spleen, neonate N10 +318 CNhs11117+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11117/summary/coverage+.w5 768 384 1.0 sum 319 CAGE:liver, neonate N00 +319 CNhs11117- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11117/summary/coverage-.w5 768 384 1.0 sum 318 CAGE:liver, neonate N00 +320 CNhs11118+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11118/summary/coverage+.w5 768 384 1.0 sum 321 CAGE:heart, neonate N10 +321 CNhs11118- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11118/summary/coverage-.w5 768 384 1.0 sum 320 CAGE:heart, neonate N10 +322 CNhs11119+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11119/summary/coverage+.w5 768 384 1.0 sum 323 CAGE:lung, neonate N25 +323 CNhs11119- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11119/summary/coverage-.w5 768 384 1.0 sum 322 CAGE:lung, neonate N25 +324 CNhs11121+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11121/summary/coverage+.w5 768 384 1.0 sum 325 CAGE:intestine, neonate N25 +325 CNhs11121- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11121/summary/coverage-.w5 768 384 1.0 sum 324 CAGE:intestine, neonate N25 +326 CNhs11122+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11122/summary/coverage+.w5 768 384 1.0 sum 327 CAGE:kidney, neonate N25 +327 CNhs11122- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11122/summary/coverage-.w5 768 384 1.0 sum 326 CAGE:kidney, neonate N25 +328 CNhs11123+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11123/summary/coverage+.w5 768 384 1.0 sum 329 CAGE:liver, neonate N03 +329 CNhs11123- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11123/summary/coverage-.w5 768 384 1.0 sum 328 CAGE:liver, neonate N03 +330 CNhs11124+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11124/summary/coverage+.w5 768 384 1.0 sum 331 CAGE:skin, neonate N00 +331 CNhs11124- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11124/summary/coverage-.w5 768 384 1.0 sum 330 CAGE:skin, neonate N00 +332 CNhs11125+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11125/summary/coverage+.w5 768 384 1.0 sum 333 CAGE:thymus, neonate N25 +333 CNhs11125- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11125/summary/coverage-.w5 768 384 1.0 sum 332 CAGE:thymus, neonate N25 +334 CNhs11126+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11126/summary/coverage+.w5 768 384 1.0 sum 335 CAGE:intestine, neonate N00 +335 CNhs11126- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11126/summary/coverage-.w5 768 384 1.0 sum 334 CAGE:intestine, neonate N00 +336 CNhs11127+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11127/summary/coverage+.w5 768 384 1.0 sum 337 CAGE:heart, neonate N20 +337 CNhs11127- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11127/summary/coverage-.w5 768 384 1.0 sum 336 CAGE:heart, neonate N20 +338 CNhs11129+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11129/summary/coverage+.w5 768 384 1.0 sum 339 CAGE:muscle (biceps femoris), neonate N30 +339 CNhs11129- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11129/summary/coverage-.w5 768 384 1.0 sum 338 CAGE:muscle (biceps femoris), neonate N30 +340 CNhs11130+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11130/summary/coverage+.w5 768 384 1.0 sum 341 CAGE:testis, neonate N30 +341 CNhs11130- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11130/summary/coverage-.w5 768 384 1.0 sum 340 CAGE:testis, neonate N30 +342 CNhs11131+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11131/summary/coverage+.w5 768 384 1.0 sum 343 CAGE:intestine, neonate N30 +343 CNhs11131- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11131/summary/coverage-.w5 768 384 1.0 sum 342 CAGE:intestine, neonate N30 +344 CNhs11132+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11132/summary/coverage+.w5 768 384 1.0 sum 345 CAGE:thymus, neonate N30 +345 CNhs11132- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11132/summary/coverage-.w5 768 384 1.0 sum 344 CAGE:thymus, neonate N30 +346 CNhs11133+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11133/summary/coverage+.w5 768 384 1.0 sum 347 CAGE:lung, neonate N30 +347 CNhs11133- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11133/summary/coverage-.w5 768 384 1.0 sum 346 CAGE:lung, neonate N30 +348 CNhs11134+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11134/summary/coverage+.w5 768 384 1.0 sum 349 CAGE:stomach, neonate N30 +349 CNhs11134- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11134/summary/coverage-.w5 768 384 1.0 sum 348 CAGE:stomach, neonate N30 +350 CNhs11135+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11135/summary/coverage+.w5 768 384 1.0 sum 351 CAGE:cerebellum, neonate N30 +351 CNhs11135- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11135/summary/coverage-.w5 768 384 1.0 sum 350 CAGE:cerebellum, neonate N30 +352 CNhs11136+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11136/summary/coverage+.w5 768 384 1.0 sum 353 CAGE:pancreas, neonate N16 +353 CNhs11136- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11136/summary/coverage-.w5 768 384 1.0 sum 352 CAGE:pancreas, neonate N16 +354 CNhs11137+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11137/summary/coverage+.w5 768 384 1.0 sum 355 CAGE:thymus, neonate N03 +355 CNhs11137- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11137/summary/coverage-.w5 768 384 1.0 sum 354 CAGE:thymus, neonate N03 +356 CNhs11138+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11138/summary/coverage+.w5 768 384 1.0 sum 357 CAGE:pancreas, neonate N01 +357 CNhs11138- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11138/summary/coverage-.w5 768 384 1.0 sum 356 CAGE:pancreas, neonate N01 +358 CNhs11139+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11139/summary/coverage+.w5 768 384 1.0 sum 359 CAGE:pancreas, neonate N02 +359 CNhs11139- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11139/summary/coverage-.w5 768 384 1.0 sum 358 CAGE:pancreas, neonate N02 +360 CNhs11140+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11140/summary/coverage+.w5 768 384 1.0 sum 361 CAGE:eyeball, neonate N01 +361 CNhs11140- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11140/summary/coverage-.w5 768 384 1.0 sum 360 CAGE:eyeball, neonate N01 +362 CNhs11181+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11181/summary/coverage+.w5 768 384 1.0 sum 363 CAGE:thymus, neonate N02 +363 CNhs11181- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11181/summary/coverage-.w5 768 384 1.0 sum 362 CAGE:thymus, neonate N02 +364 CNhs11182+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11182/summary/coverage+.w5 768 384 1.0 sum 365 CAGE:pancreas, neonate N30 +365 CNhs11182- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11182/summary/coverage-.w5 768 384 1.0 sum 364 CAGE:pancreas, neonate N30 +366 CNhs11186+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11186/summary/coverage+.w5 768 384 1.0 sum 367 CAGE:thymus, neonate N20 +367 CNhs11186- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11186/summary/coverage-.w5 768 384 1.0 sum 366 CAGE:thymus, neonate N20 +368 CNhs11187+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11187/summary/coverage+.w5 768 384 1.0 sum 369 CAGE:intestine, neonate N20 +369 CNhs11187- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11187/summary/coverage-.w5 768 384 1.0 sum 368 CAGE:intestine, neonate N20 +370 CNhs11188+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11188/summary/coverage+.w5 768 384 1.0 sum 371 CAGE:eyeball, neonate N16 +371 CNhs11188- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11188/summary/coverage-.w5 768 384 1.0 sum 370 CAGE:eyeball, neonate N16 +372 CNhs11189+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11189/summary/coverage+.w5 768 384 1.0 sum 373 CAGE:testis, neonate N00 +373 CNhs11189- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11189/summary/coverage-.w5 768 384 1.0 sum 372 CAGE:testis, neonate N00 +374 CNhs11190+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11190/summary/coverage+.w5 768 384 1.0 sum 375 CAGE:pituitary gland, neonate N00 +375 CNhs11190- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11190/summary/coverage-.w5 768 384 1.0 sum 374 CAGE:pituitary gland, neonate N00 +376 CNhs11191+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11191/summary/coverage+.w5 768 384 1.0 sum 377 CAGE:adrenal gland, neonate N00 +377 CNhs11191- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11191/summary/coverage-.w5 768 384 1.0 sum 376 CAGE:adrenal gland, neonate N00 +378 CNhs11192+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11192/summary/coverage+.w5 768 384 1.0 sum 379 CAGE:intestine, neonate N01 +379 CNhs11192- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11192/summary/coverage-.w5 768 384 1.0 sum 378 CAGE:intestine, neonate N01 +380 CNhs11193+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11193/summary/coverage+.w5 768 384 1.0 sum 381 CAGE:stomach, neonate N03 +381 CNhs11193- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11193/summary/coverage-.w5 768 384 1.0 sum 380 CAGE:stomach, neonate N03 +382 CNhs11194+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11194/summary/coverage+.w5 768 384 1.0 sum 383 CAGE:thymus, neonate N10 +383 CNhs11194- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11194/summary/coverage-.w5 768 384 1.0 sum 382 CAGE:thymus, neonate N10 +384 CNhs11195+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11195/summary/coverage+.w5 768 384 1.0 sum 385 CAGE:bone (os femoris), neonate N20 +385 CNhs11195- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11195/summary/coverage-.w5 768 384 1.0 sum 384 CAGE:bone (os femoris), neonate N20 +386 CNhs11196+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11196/summary/coverage+.w5 768 384 1.0 sum 387 CAGE:heart, neonate N25 +387 CNhs11196- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11196/summary/coverage-.w5 768 384 1.0 sum 386 CAGE:heart, neonate N25 +388 CNhs11197+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11197/summary/coverage+.w5 768 384 1.0 sum 389 CAGE:thymus, neonate N06 +389 CNhs11197- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11197/summary/coverage-.w5 768 384 1.0 sum 388 CAGE:thymus, neonate N06 +390 CNhs11198+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11198/summary/coverage+.w5 768 384 1.0 sum 391 CAGE:liver, neonate N25 +391 CNhs11198- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11198/summary/coverage-.w5 768 384 1.0 sum 390 CAGE:liver, neonate N25 +392 CNhs11199+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11199/summary/coverage+.w5 768 384 1.0 sum 393 CAGE:epididymis and seminiferous tubule, neonate N30 +393 CNhs11199- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11199/summary/coverage-.w5 768 384 1.0 sum 392 CAGE:epididymis and seminiferous tubule, neonate N30 +394 CNhs11200+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11200/summary/coverage+.w5 768 384 1.0 sum 395 CAGE:medulla oblongata, neonate N30 +395 CNhs11200- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11200/summary/coverage-.w5 768 384 1.0 sum 394 CAGE:medulla oblongata, neonate N30 +396 CNhs11201+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11201/summary/coverage+.w5 768 384 1.0 sum 397 CAGE:diencephalon, neonate N30 +397 CNhs11201- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11201/summary/coverage-.w5 768 384 1.0 sum 396 CAGE:diencephalon, neonate N30 +398 CNhs11202+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11202/summary/coverage+.w5 768 384 1.0 sum 399 CAGE:heart, neonate N30 +399 CNhs11202- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11202/summary/coverage-.w5 768 384 1.0 sum 398 CAGE:heart, neonate N30 +400 CNhs11203+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11203/summary/coverage+.w5 768 384 1.0 sum 401 CAGE:kidney, neonate N30 +401 CNhs11203- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11203/summary/coverage-.w5 768 384 1.0 sum 400 CAGE:kidney, neonate N30 +402 CNhs11204+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11204/summary/coverage+.w5 768 384 1.0 sum 403 CAGE:testis, neonate N10 +403 CNhs11204- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11204/summary/coverage-.w5 768 384 1.0 sum 402 CAGE:testis, neonate N10 +404 CNhs11205+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11205/summary/coverage+.w5 768 384 1.0 sum 405 CAGE:eyeball, neonate N02 +405 CNhs11205- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11205/summary/coverage-.w5 768 384 1.0 sum 404 CAGE:eyeball, neonate N02 +406 CNhs11206+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11206/summary/coverage+.w5 768 384 1.0 sum 407 CAGE:kidney, neonate N10 +407 CNhs11206- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11206/summary/coverage-.w5 768 384 1.0 sum 406 CAGE:kidney, neonate N10 +408 CNhs11207+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11207/summary/coverage+.w5 768 384 1.0 sum 409 CAGE:eyeball, neonate N00 +409 CNhs11207- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11207/summary/coverage-.w5 768 384 1.0 sum 408 CAGE:eyeball, neonate N00 +410 CNhs11209+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11209/summary/coverage+.w5 768 384 1.0 sum 411 CAGE:heart, neonate N16 +411 CNhs11209- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11209/summary/coverage-.w5 768 384 1.0 sum 410 CAGE:heart, neonate N16 +412 CNhs11210+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11210/summary/coverage+.w5 768 384 1.0 sum 413 CAGE:stomach, neonate N07 +413 CNhs11210- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11210/summary/coverage-.w5 768 384 1.0 sum 412 CAGE:stomach, neonate N07 +414 CNhs11211+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11211/summary/coverage+.w5 768 384 1.0 sum 415 CAGE:thymus, neonate N07 +415 CNhs11211- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11211/summary/coverage-.w5 768 384 1.0 sum 414 CAGE:thymus, neonate N07 +416 CNhs11212+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11212/summary/coverage+.w5 768 384 1.0 sum 417 CAGE:lung, neonate N06 +417 CNhs11212- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11212/summary/coverage-.w5 768 384 1.0 sum 416 CAGE:lung, neonate N06 +418 CNhs11213+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11213/summary/coverage+.w5 768 384 1.0 sum 419 CAGE:heart, neonate N00 +419 CNhs11213- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11213/summary/coverage-.w5 768 384 1.0 sum 418 CAGE:heart, neonate N00 +420 CNhs11214+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11214/summary/coverage+.w5 768 384 1.0 sum 421 CAGE:kidney, neonate N00 +421 CNhs11214- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11214/summary/coverage-.w5 768 384 1.0 sum 420 CAGE:kidney, neonate N00 +422 CNhs11215+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11215/summary/coverage+.w5 768 384 1.0 sum 423 CAGE:skin, neonate N03 +423 CNhs11215- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11215/summary/coverage-.w5 768 384 1.0 sum 422 CAGE:skin, neonate N03 +424 CNhs11217+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11217/summary/coverage+.w5 768 384 1.0 sum 425 CAGE:ovary, neonate N00 +425 CNhs11217- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11217/summary/coverage-.w5 768 384 1.0 sum 424 CAGE:ovary, neonate N00 +426 CNhs11218+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11218/summary/coverage+.w5 768 384 1.0 sum 427 CAGE:epididymis and seminiferous tubule, neonate N00 +427 CNhs11218- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11218/summary/coverage-.w5 768 384 1.0 sum 426 CAGE:epididymis and seminiferous tubule, neonate N00 +428 CNhs11219+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11219/summary/coverage+.w5 768 384 1.0 sum 429 CAGE:lung, neonate N10 +429 CNhs11219- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11219/summary/coverage-.w5 768 384 1.0 sum 428 CAGE:lung, neonate N10 +430 CNhs11220+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11220/summary/coverage+.w5 768 384 1.0 sum 431 CAGE:liver, neonate N20 +431 CNhs11220- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11220/summary/coverage-.w5 768 384 1.0 sum 430 CAGE:liver, neonate N20 +432 CNhs11221+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11221/summary/coverage+.w5 768 384 1.0 sum 433 CAGE:heart, neonate N03 +433 CNhs11221- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11221/summary/coverage-.w5 768 384 1.0 sum 432 CAGE:heart, neonate N03 +434 CNhs11222+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11222/summary/coverage+.w5 768 384 1.0 sum 435 CAGE:testis, neonate N07 +435 CNhs11222- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11222/summary/coverage-.w5 768 384 1.0 sum 434 CAGE:testis, neonate N07 +436 CNhs11223+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11223/summary/coverage+.w5 768 384 1.0 sum 437 CAGE:adrenal gland, neonate N25 +437 CNhs11223- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11223/summary/coverage-.w5 768 384 1.0 sum 436 CAGE:adrenal gland, neonate N25 +438 CNhs11224+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11224/summary/coverage+.w5 768 384 1.0 sum 439 CAGE:lung, neonate N00 +439 CNhs11224- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11224/summary/coverage-.w5 768 384 1.0 sum 438 CAGE:lung, neonate N00 +440 CNhs11225+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11225/summary/coverage+.w5 768 384 1.0 sum 441 CAGE:bone (os femoris), neonate N16 +441 CNhs11225- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11225/summary/coverage-.w5 768 384 1.0 sum 440 CAGE:bone (os femoris), neonate N16 +442 CNhs11226+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11226/summary/coverage+.w5 768 384 1.0 sum 443 CAGE:corpus striatum, neonate N00 +443 CNhs11226- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11226/summary/coverage-.w5 768 384 1.0 sum 442 CAGE:corpus striatum, neonate N00 +444 CNhs11227+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11227/summary/coverage+.w5 768 384 1.0 sum 445 CAGE:bone (os femoris), neonate N02 +445 CNhs11227- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11227/summary/coverage-.w5 768 384 1.0 sum 444 CAGE:bone (os femoris), neonate N02 +446 CNhs11228+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11228/summary/coverage+.w5 768 384 1.0 sum 447 CAGE:hippocampus, neonate N00 +447 CNhs11228- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11228/summary/coverage-.w5 768 384 1.0 sum 446 CAGE:hippocampus, neonate N00 +448 CNhs11297+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11297/summary/coverage+.w5 768 384 1.0 sum 449 CAGE:Mouse Aortic Smooth Muscle cells, +449 CNhs11297- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11297/summary/coverage-.w5 768 384 1.0 sum 448 CAGE:Mouse Aortic Smooth Muscle cells, +450 CNhs11915+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11915/summary/coverage+.w5 768 384 1.0 sum 451 CAGE:Astrocytes, +451 CNhs11915- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11915/summary/coverage-.w5 768 384 1.0 sum 450 CAGE:Astrocytes, +452 CNhs11928+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11928/summary/coverage+.w5 768 384 1.0 sum 453 CAGE:granulocyte macrophage progenitor GMP, biol_ +453 CNhs11928- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11928/summary/coverage-.w5 768 384 1.0 sum 452 CAGE:granulocyte macrophage progenitor GMP, biol_ +454 CNhs11929+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11929/summary/coverage+.w5 768 384 1.0 sum 455 CAGE:Inner ear stem cells, 1st generation stem cells, pool1 +455 CNhs11929- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11929/summary/coverage-.w5 768 384 1.0 sum 454 CAGE:Inner ear stem cells, 1st generation stem cells, pool1 +456 CNhs11947+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11947/summary/coverage+.w5 768 384 1.0 sum 457 CAGE:Mouse Neurons - cortical, +457 CNhs11947- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs11947/summary/coverage-.w5 768 384 1.0 sum 456 CAGE:Mouse Neurons - cortical, +458 CNhs12076+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12076/summary/coverage+.w5 768 384 1.0 sum 459 CAGE:Mouse Astrocytes - cerebellar, +459 CNhs12076- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12076/summary/coverage-.w5 768 384 1.0 sum 458 CAGE:Mouse Astrocytes - cerebellar, +460 CNhs12077+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12077/summary/coverage+.w5 768 384 1.0 sum 461 CAGE:Mouse Astrocytes - hippocampus, +461 CNhs12077- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12077/summary/coverage-.w5 768 384 1.0 sum 460 CAGE:Mouse Astrocytes - hippocampus, +462 CNhs12107+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12078/summary/coverage+.w5 768 384 1.0 sum 463 CAGE:Mouse Astrocytes, +463 CNhs12107- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12078/summary/coverage-.w5 768 384 1.0 sum 462 CAGE:Mouse Astrocytes, +464 CNhs12108+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12108/summary/coverage+.w5 768 384 1.0 sum 465 CAGE:Mouse Granule cells, +465 CNhs12108- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12108/summary/coverage-.w5 768 384 1.0 sum 464 CAGE:Mouse Granule cells, +466 CNhs12109+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12109/summary/coverage+.w5 768 384 1.0 sum 467 CAGE:Mouse Meningeal cells, +467 CNhs12109- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12109/summary/coverage-.w5 768 384 1.0 sum 466 CAGE:Mouse Meningeal cells, +468 CNhs12110+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12110/summary/coverage+.w5 768 384 1.0 sum 469 CAGE:Mouse Neurons - hippocampal, +469 CNhs12110- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12110/summary/coverage-.w5 768 384 1.0 sum 468 CAGE:Mouse Neurons - hippocampal, +470 CNhs12134+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12111/summary/coverage+.w5 768 384 1.0 sum 471 CAGE:Mouse Neurons - striatal, +471 CNhs12134- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12111/summary/coverage-.w5 768 384 1.0 sum 470 CAGE:Mouse Neurons - striatal, +472 CNhs12632+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12113/summary/coverage+.w5 768 384 1.0 sum 473 CAGE:Mouse Neurons - ventral spinal cord, +473 CNhs12632- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12113/summary/coverage-.w5 768 384 1.0 sum 472 CAGE:Mouse Neurons - ventral spinal cord, +474 CNhs12507+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12115/summary/coverage+.w5 768 384 1.0 sum 475 CAGE:Mouse Schwann, +475 CNhs12507- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12115/summary/coverage-.w5 768 384 1.0 sum 474 CAGE:Mouse Schwann, +476 CNhs12130+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12130/summary/coverage+.w5 768 384 1.0 sum 477 CAGE:Mouse Embryonic fibroblasts, +477 CNhs12130- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12130/summary/coverage-.w5 768 384 1.0 sum 476 CAGE:Mouse Embryonic fibroblasts, +478 CNhs12189+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12189/summary/coverage+.w5 768 384 1.0 sum 479 CAGE:Inner ear stem cells, differentiation, day03, pool1 +479 CNhs12189- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12189/summary/coverage-.w5 768 384 1.0 sum 478 CAGE:Inner ear stem cells, differentiation, day03, pool1 +480 CNhs12190+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12190/summary/coverage+.w5 768 384 1.0 sum 481 CAGE:Inner ear stem cells, differentiation, day10, pool1 +481 CNhs12190- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12190/summary/coverage-.w5 768 384 1.0 sum 480 CAGE:Inner ear stem cells, differentiation, day10, pool1 +482 CNhs12198+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12198/summary/coverage+.w5 768 384 1.0 sum 483 CAGE:MC1+Gr1+ myeloid-derived suppressor cells cancer, (0127 3LL) +483 CNhs12198- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12198/summary/coverage-.w5 768 384 1.0 sum 482 CAGE:MC1+Gr1+ myeloid-derived suppressor cells cancer, (0127 3LL) +484 CNhs12203+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12203/summary/coverage+.w5 768 384 1.0 sum 485 CAGE:common myeloid progenitor CMP, biol_ +485 CNhs12203- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12203/summary/coverage-.w5 768 384 1.0 sum 484 CAGE:common myeloid progenitor CMP, biol_ +486 CNhs12355+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12353/summary/coverage+.w5 768 384 1.0 sum 487 CAGE:Mouse Cardiac Myocytes, +487 CNhs12355- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12353/summary/coverage-.w5 768 384 1.0 sum 486 CAGE:Mouse Cardiac Myocytes, +488 CNhs12508+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12508/summary/coverage+.w5 768 384 1.0 sum 489 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_rep1 +489 CNhs12508- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12508/summary/coverage-.w5 768 384 1.0 sum 488 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_rep1 +490 CNhs12515+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12515/summary/coverage+.w5 768 384 1.0 sum 491 CAGE:natural helper cells, naive, biol_, tech_rep1 +491 CNhs12515- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12515/summary/coverage-.w5 768 384 1.0 sum 490 CAGE:natural helper cells, naive, biol_, tech_rep1 +492 CNhs12532+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12532/summary/coverage+.w5 768 384 1.0 sum 493 CAGE:Sox2+ Supporting cells - organ of corti, pool1 +493 CNhs12532- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12532/summary/coverage-.w5 768 384 1.0 sum 492 CAGE:Sox2+ Supporting cells - organ of corti, pool1 +494 CNhs12533+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12533/summary/coverage+.w5 768 384 1.0 sum 495 CAGE:Atoh1+ Inner ear hair cells - organ of corti, pool1 +495 CNhs12533- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12533/summary/coverage-.w5 768 384 1.0 sum 494 CAGE:Atoh1+ Inner ear hair cells - organ of corti, pool1 +496 CNhs12534+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12534/summary/coverage+.w5 768 384 1.0 sum 497 CAGE:stem cell (cKit+ Sca1- lineage-) KSL, biol_ +497 CNhs12534- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12534/summary/coverage-.w5 768 384 1.0 sum 496 CAGE:stem cell (cKit+ Sca1- lineage-) KSL, biol_ +498 CNhs12539+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12539/summary/coverage+.w5 768 384 1.0 sum 499 CAGE:MC1+Gr1+ myeloid-derived suppressor cells cancer, (10,11,12 3LL) +499 CNhs12539- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12539/summary/coverage-.w5 768 384 1.0 sum 498 CAGE:MC1+Gr1+ myeloid-derived suppressor cells cancer, (10,11,12 3LL) +500 CNhs12540+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12540/summary/coverage+.w5 768 384 1.0 sum 501 CAGE:MC1+Gr1+ myeloid-derived suppressor cells control, (4,5,6PBS) +501 CNhs12540- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12540/summary/coverage-.w5 768 384 1.0 sum 500 CAGE:MC1+Gr1+ myeloid-derived suppressor cells control, (4,5,6PBS) +502 CNhs12541+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12541/summary/coverage+.w5 768 384 1.0 sum 503 CAGE:MC1+Gr1+ myeloid-derived suppressor cells control, (0127 PBS) +503 CNhs12541- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12541/summary/coverage-.w5 768 384 1.0 sum 502 CAGE:MC1+Gr1+ myeloid-derived suppressor cells control, (0127 PBS) +504 CNhs12542+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12542/summary/coverage+.w5 768 384 1.0 sum 505 CAGE:MC1+Gr1+ myeloid-derived suppressor cells cancer, (0128 3LL) +505 CNhs12542- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12542/summary/coverage-.w5 768 384 1.0 sum 504 CAGE:MC1+Gr1+ myeloid-derived suppressor cells cancer, (0128 3LL) +506 CNhs12543+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12543/summary/coverage+.w5 768 384 1.0 sum 507 CAGE:MC1+Gr1+ myeloid-derived suppressor cells control, (0128 PBS) +507 CNhs12543- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12543/summary/coverage-.w5 768 384 1.0 sum 506 CAGE:MC1+Gr1+ myeloid-derived suppressor cells control, (0128 PBS) +508 CNhs12544+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12544/summary/coverage+.w5 768 384 1.0 sum 509 CAGE:Inner ear stem cells, 4th generation stem cells, pool1 +509 CNhs12544- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12544/summary/coverage-.w5 768 384 1.0 sum 508 CAGE:Inner ear stem cells, 4th generation stem cells, pool1 +510 CNhs12555+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12555/summary/coverage+.w5 768 384 1.0 sum 511 CAGE:Lgr5 positive intestinal stem cells, pool1 +511 CNhs12555- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12555/summary/coverage-.w5 768 384 1.0 sum 510 CAGE:Lgr5 positive intestinal stem cells, pool1 +512 CNhs12556+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12556/summary/coverage+.w5 768 384 1.0 sum 513 CAGE:Lgr5 positive intestinal stem cells, pool2 +513 CNhs12556- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12556/summary/coverage-.w5 768 384 1.0 sum 512 CAGE:Lgr5 positive intestinal stem cells, pool2 +514 CNhs12557+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12557/summary/coverage+.w5 768 384 1.0 sum 515 CAGE:Lgr5 positive intestinal stem cells, pool3 +515 CNhs12557- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12557/summary/coverage-.w5 768 384 1.0 sum 514 CAGE:Lgr5 positive intestinal stem cells, pool3 +516 CNhs14334+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12576/summary/coverage+.w5 768 384 1.0 sum 517 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_ +517 CNhs14334- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12576/summary/coverage-.w5 768 384 1.0 sum 516 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_ +518 CNhs12578+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12578/summary/coverage+.w5 768 384 1.0 sum 519 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_rep1 +519 CNhs12578- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12578/summary/coverage-.w5 768 384 1.0 sum 518 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_rep1 +520 CNhs12579+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12579/summary/coverage+.w5 768 384 1.0 sum 521 CAGE:natural helper cells, IL33 treated, 01hr, biol_, tech_ +521 CNhs12579- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12579/summary/coverage-.w5 768 384 1.0 sum 520 CAGE:natural helper cells, IL33 treated, 01hr, biol_, tech_ +522 CNhs12821+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12612/summary/coverage+.w5 768 384 1.0 sum 523 CAGE:Mouse Neurons - substantia nigra, , tech_ +523 CNhs12821- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12612/summary/coverage-.w5 768 384 1.0 sum 522 CAGE:Mouse Neurons - substantia nigra, , tech_ +524 CNhs12643+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12614/summary/coverage+.w5 768 384 1.0 sum 525 CAGE:Mouse Neurons - substantia nigra, +525 CNhs12643- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12614/summary/coverage-.w5 768 384 1.0 sum 524 CAGE:Mouse Neurons - substantia nigra, +526 CNhs14554+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12615/summary/coverage+.w5 768 384 1.0 sum 527 CAGE:Mouse hepatocyte, +527 CNhs14554- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12615/summary/coverage-.w5 768 384 1.0 sum 526 CAGE:Mouse hepatocyte, +528 CNhs12628+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12616/summary/coverage+.w5 768 384 1.0 sum 529 CAGE:Mouse Mesenchymal stem cells - bone marrow derived, +529 CNhs12628- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12616/summary/coverage-.w5 768 384 1.0 sum 528 CAGE:Mouse Mesenchymal stem cells - bone marrow derived, +530 CNhs12629+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12617/summary/coverage+.w5 768 384 1.0 sum 531 CAGE:Mouse Microglia, +531 CNhs12629- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12617/summary/coverage-.w5 768 384 1.0 sum 530 CAGE:Mouse Microglia, +532 CNhs12618+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12618/summary/coverage+.w5 768 384 1.0 sum 533 CAGE:Mouse Neurons - dorsal spinal cord, +533 CNhs12618- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12618/summary/coverage-.w5 768 384 1.0 sum 532 CAGE:Mouse Neurons - dorsal spinal cord, +534 CNhs12631+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12619/summary/coverage+.w5 768 384 1.0 sum 535 CAGE:Mouse Neurons - raphe, +535 CNhs12631- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12619/summary/coverage-.w5 768 384 1.0 sum 534 CAGE:Mouse Neurons - raphe, +536 CNhs12818+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12818/summary/coverage+.w5 768 384 1.0 sum 537 CAGE:cerebellum, embryo E17, biol_ (E17R1) +537 CNhs12818- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12818/summary/coverage-.w5 768 384 1.0 sum 536 CAGE:cerebellum, embryo E17, biol_ (E17R1) +538 CNhs12819+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12819/summary/coverage+.w5 768 384 1.0 sum 539 CAGE:cerebellum, neonate N06, biol_ (P6R1) +539 CNhs12819- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12819/summary/coverage-.w5 768 384 1.0 sum 538 CAGE:cerebellum, neonate N06, biol_ (P6R1) +540 CNhs12820+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12820/summary/coverage+.w5 768 384 1.0 sum 541 CAGE:cerebellum, neonate N09, biol_ (P9R1) +541 CNhs12820- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12820/summary/coverage-.w5 768 384 1.0 sum 540 CAGE:cerebellum, neonate N09, biol_ (P9R1) +542 CNhs12923+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12923/summary/coverage+.w5 768 384 1.0 sum 543 CAGE:Neurons - substantia nigra, , tech_ +543 CNhs12923- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12923/summary/coverage-.w5 768 384 1.0 sum 542 CAGE:Neurons - substantia nigra, , tech_ +544 CNhs12956+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12956/summary/coverage+.w5 768 384 1.0 sum 545 CAGE:cerebellum, embryo E11, biol_ (E11R1) +545 CNhs12956- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12956/summary/coverage-.w5 768 384 1.0 sum 544 CAGE:cerebellum, embryo E11, biol_ (E11R1) +546 CNhs12957+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12957/summary/coverage+.w5 768 384 1.0 sum 547 CAGE:cerebellum, embryo E12, biol_ (E12R1) +547 CNhs12957- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12957/summary/coverage-.w5 768 384 1.0 sum 546 CAGE:cerebellum, embryo E12, biol_ (E12R1) +548 CNhs12958+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12958/summary/coverage+.w5 768 384 1.0 sum 549 CAGE:cerebellum, embryo E13, biol_ (E13R1) +549 CNhs12958- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12958/summary/coverage-.w5 768 384 1.0 sum 548 CAGE:cerebellum, embryo E13, biol_ (E13R1) +550 CNhs12960+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12960/summary/coverage+.w5 768 384 1.0 sum 551 CAGE:cerebellum, embryo E14, biol_ (E14R1) +551 CNhs12960- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12960/summary/coverage-.w5 768 384 1.0 sum 550 CAGE:cerebellum, embryo E14, biol_ (E14R1) +552 CNhs12961+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12961/summary/coverage+.w5 768 384 1.0 sum 553 CAGE:cerebellum, embryo E15, biol_ (E15R1) +553 CNhs12961- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12961/summary/coverage-.w5 768 384 1.0 sum 552 CAGE:cerebellum, embryo E15, biol_ (E15R1) +554 CNhs12962+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12962/summary/coverage+.w5 768 384 1.0 sum 555 CAGE:cerebellum, embryo E18, biol_ (E18R1) +555 CNhs12962- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12962/summary/coverage-.w5 768 384 1.0 sum 554 CAGE:cerebellum, embryo E18, biol_ (E18R1) +556 CNhs12963+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12963/summary/coverage+.w5 768 384 1.0 sum 557 CAGE:cerebellum, neonate N00, biol_ (P0R1) +557 CNhs12963- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs12963/summary/coverage-.w5 768 384 1.0 sum 556 CAGE:cerebellum, neonate N00, biol_ (P0R1) +558 CNhs13000+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13000/summary/coverage+.w5 768 384 1.0 sum 559 CAGE:cerebellum, embryo E16, biol_ (E16R1) +559 CNhs13000- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13000/summary/coverage-.w5 768 384 1.0 sum 558 CAGE:cerebellum, embryo E16, biol_ (E16R1) +560 CNhs13001+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13001/summary/coverage+.w5 768 384 1.0 sum 561 CAGE:cerebellum, neonate N03, biol_ (P3R1) +561 CNhs13001- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13001/summary/coverage-.w5 768 384 1.0 sum 560 CAGE:cerebellum, neonate N03, biol_ (P3R1) +562 CNhs13002+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13002/summary/coverage+.w5 768 384 1.0 sum 563 CAGE:cerebellum, embryo E11, biol_ (E11R2) +563 CNhs13002- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13002/summary/coverage-.w5 768 384 1.0 sum 562 CAGE:cerebellum, embryo E11, biol_ (E11R2) +564 CNhs13003+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13003/summary/coverage+.w5 768 384 1.0 sum 565 CAGE:cerebellum, embryo E12, biol_ (E12R2) +565 CNhs13003- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13003/summary/coverage-.w5 768 384 1.0 sum 564 CAGE:cerebellum, embryo E12, biol_ (E12R2) +566 CNhs13004+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13004/summary/coverage+.w5 768 384 1.0 sum 567 CAGE:cerebellum, embryo E13, biol_ (E13R2) +567 CNhs13004- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13004/summary/coverage-.w5 768 384 1.0 sum 566 CAGE:cerebellum, embryo E13, biol_ (E13R2) +568 CNhs13005+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13005/summary/coverage+.w5 768 384 1.0 sum 569 CAGE:cerebellum, embryo E14, biol_ (E14R2) +569 CNhs13005- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13005/summary/coverage-.w5 768 384 1.0 sum 568 CAGE:cerebellum, embryo E14, biol_ (E14R2) +570 CNhs13006+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13006/summary/coverage+.w5 768 384 1.0 sum 571 CAGE:cerebellum, embryo E15, biol_ (E15R2) +571 CNhs13006- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13006/summary/coverage-.w5 768 384 1.0 sum 570 CAGE:cerebellum, embryo E15, biol_ (E15R2) +572 CNhs13007+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13007/summary/coverage+.w5 768 384 1.0 sum 573 CAGE:cerebellum, embryo E16, biol_ (E16R2) +573 CNhs13007- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13007/summary/coverage-.w5 768 384 1.0 sum 572 CAGE:cerebellum, embryo E16, biol_ (E16R2) +574 CNhs13008+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13008/summary/coverage+.w5 768 384 1.0 sum 575 CAGE:cerebellum, embryo E17, biol_ (E17R2) +575 CNhs13008- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13008/summary/coverage-.w5 768 384 1.0 sum 574 CAGE:cerebellum, embryo E17, biol_ (E17R2) +576 CNhs13009+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13009/summary/coverage+.w5 768 384 1.0 sum 577 CAGE:cerebellum, embryo E18, biol_ (E18R2) +577 CNhs13009- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13009/summary/coverage-.w5 768 384 1.0 sum 576 CAGE:cerebellum, embryo E18, biol_ (E18R2) +578 CNhs13010+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13010/summary/coverage+.w5 768 384 1.0 sum 579 CAGE:cerebellum, neonate N00, biol_ (P0R2) +579 CNhs13010- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13010/summary/coverage-.w5 768 384 1.0 sum 578 CAGE:cerebellum, neonate N00, biol_ (P0R2) +580 CNhs13011+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13011/summary/coverage+.w5 768 384 1.0 sum 581 CAGE:cerebellum, neonate N03, biol_ (P3R2) +581 CNhs13011- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13011/summary/coverage-.w5 768 384 1.0 sum 580 CAGE:cerebellum, neonate N03, biol_ (P3R2) +582 CNhs13012+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13012/summary/coverage+.w5 768 384 1.0 sum 583 CAGE:cerebellum, neonate N06, biol_ (P6R2) +583 CNhs13012- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13012/summary/coverage-.w5 768 384 1.0 sum 582 CAGE:cerebellum, neonate N06, biol_ (P6R2) +584 CNhs13013+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13013/summary/coverage+.w5 768 384 1.0 sum 585 CAGE:cerebellum, neonate N09, biol_ (P9R2) +585 CNhs13013- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13013/summary/coverage-.w5 768 384 1.0 sum 584 CAGE:cerebellum, neonate N09, biol_ (P9R2) +586 CNhs13014+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13014/summary/coverage+.w5 768 384 1.0 sum 587 CAGE:cerebellum, embryo E11, biol_ (E11R3) +587 CNhs13014- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13014/summary/coverage-.w5 768 384 1.0 sum 586 CAGE:cerebellum, embryo E11, biol_ (E11R3) +588 CNhs13015+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13015/summary/coverage+.w5 768 384 1.0 sum 589 CAGE:cerebellum, embryo E12, biol_ (E12R3) +589 CNhs13015- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13015/summary/coverage-.w5 768 384 1.0 sum 588 CAGE:cerebellum, embryo E12, biol_ (E12R3) +590 CNhs13016+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13016/summary/coverage+.w5 768 384 1.0 sum 591 CAGE:cerebellum, embryo E13, biol_ (E13R3) +591 CNhs13016- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13016/summary/coverage-.w5 768 384 1.0 sum 590 CAGE:cerebellum, embryo E13, biol_ (E13R3) +592 CNhs13017+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13017/summary/coverage+.w5 768 384 1.0 sum 593 CAGE:cerebellum, embryo E14, biol_ (E14R3) +593 CNhs13017- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13017/summary/coverage-.w5 768 384 1.0 sum 592 CAGE:cerebellum, embryo E14, biol_ (E14R3) +594 CNhs13018+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13018/summary/coverage+.w5 768 384 1.0 sum 595 CAGE:cerebellum, embryo E15, biol_ (E15R3) +595 CNhs13018- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13018/summary/coverage-.w5 768 384 1.0 sum 594 CAGE:cerebellum, embryo E15, biol_ (E15R3) +596 CNhs13019+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13019/summary/coverage+.w5 768 384 1.0 sum 597 CAGE:cerebellum, embryo E16, biol_ (E16R3) +597 CNhs13019- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13019/summary/coverage-.w5 768 384 1.0 sum 596 CAGE:cerebellum, embryo E16, biol_ (E16R3) +598 CNhs13020+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13020/summary/coverage+.w5 768 384 1.0 sum 599 CAGE:cerebellum, embryo E17, biol_ (E17R3) +599 CNhs13020- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13020/summary/coverage-.w5 768 384 1.0 sum 598 CAGE:cerebellum, embryo E17, biol_ (E17R3) +600 CNhs13021+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13021/summary/coverage+.w5 768 384 1.0 sum 601 CAGE:cerebellum, embryo E18, biol_ (E18R3) +601 CNhs13021- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13021/summary/coverage-.w5 768 384 1.0 sum 600 CAGE:cerebellum, embryo E18, biol_ (E18R3) +602 CNhs13022+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13022/summary/coverage+.w5 768 384 1.0 sum 603 CAGE:cerebellum, neonate N00, biol_ (P0R3) +603 CNhs13022- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13022/summary/coverage-.w5 768 384 1.0 sum 602 CAGE:cerebellum, neonate N00, biol_ (P0R3) +604 CNhs13024+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13024/summary/coverage+.w5 768 384 1.0 sum 605 CAGE:cerebellum, neonate N03, biol_ (P3R3) +605 CNhs13024- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13024/summary/coverage-.w5 768 384 1.0 sum 604 CAGE:cerebellum, neonate N03, biol_ (P3R3) +606 CNhs13025+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13025/summary/coverage+.w5 768 384 1.0 sum 607 CAGE:cerebellum, neonate N06, biol_ (P6R3) +607 CNhs13025- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13025/summary/coverage-.w5 768 384 1.0 sum 606 CAGE:cerebellum, neonate N06, biol_ (P6R3) +608 CNhs13026+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13026/summary/coverage+.w5 768 384 1.0 sum 609 CAGE:cerebellum, neonate N09, biol_ (P9R3) +609 CNhs13026- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13026/summary/coverage-.w5 768 384 1.0 sum 608 CAGE:cerebellum, neonate N09, biol_ (P9R3) +610 CNhs13032+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13031/summary/coverage+.w5 768 384 1.0 sum 611 CAGE:visual cortex - wildtype, neonate N15, +611 CNhs13032- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13031/summary/coverage-.w5 768 384 1.0 sum 610 CAGE:visual cortex - wildtype, neonate N15, +612 CNhs13034+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13034/summary/coverage+.w5 768 384 1.0 sum 613 CAGE:visual cortex - wildtype, neonate N30, +613 CNhs13034- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13034/summary/coverage-.w5 768 384 1.0 sum 612 CAGE:visual cortex - wildtype, neonate N30, +614 CNhs13038+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13037/summary/coverage+.w5 768 384 1.0 sum 615 CAGE:visual cortex - wildtype, neonate N60-70, +615 CNhs13038- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13037/summary/coverage-.w5 768 384 1.0 sum 614 CAGE:visual cortex - wildtype, neonate N60-70, +616 CNhs13040+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13040/summary/coverage+.w5 768 384 1.0 sum 617 CAGE:visual cortex - Mecp knockout, neonate N15, +617 CNhs13040- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13040/summary/coverage-.w5 768 384 1.0 sum 616 CAGE:visual cortex - Mecp knockout, neonate N15, +618 CNhs13042+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13042/summary/coverage+.w5 768 384 1.0 sum 619 CAGE:visual cortex - Mecp knockout, neonate N30, +619 CNhs13042- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13042/summary/coverage-.w5 768 384 1.0 sum 618 CAGE:visual cortex - Mecp knockout, neonate N30, +620 CNhs13046+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13045/summary/coverage+.w5 768 384 1.0 sum 621 CAGE:visual cortex - Mecp knockout, neonate N60-70, +621 CNhs13046- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13045/summary/coverage-.w5 768 384 1.0 sum 620 CAGE:visual cortex - Mecp knockout, neonate N60-70, +622 CNhs13079+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13079/summary/coverage+.w5 768 384 1.0 sum 623 CAGE:CD41+ megakaryocyte cancer, +623 CNhs13079- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13079/summary/coverage-.w5 768 384 1.0 sum 622 CAGE:CD41+ megakaryocyte cancer, +624 CNhs13083+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13081/summary/coverage+.w5 768 384 1.0 sum 625 CAGE:neurospheres - sympathetic neuron derived, biol_ +625 CNhs13083- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13081/summary/coverage-.w5 768 384 1.0 sum 624 CAGE:neurospheres - sympathetic neuron derived, biol_ +626 CNhs13086+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13084/summary/coverage+.w5 768 384 1.0 sum 627 CAGE:neurospheres - parasympathetic neuron derived, biol_ +627 CNhs13086- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13084/summary/coverage-.w5 768 384 1.0 sum 626 CAGE:neurospheres - parasympathetic neuron derived, biol_ +628 CNhs13089+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13087/summary/coverage+.w5 768 384 1.0 sum 629 CAGE:neurospheres - enteric neuron derived, biol_ +629 CNhs13089- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13087/summary/coverage-.w5 768 384 1.0 sum 628 CAGE:neurospheres - enteric neuron derived, biol_ +630 CNhs13196+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13196/summary/coverage+.w5 768 384 1.0 sum 631 CAGE:Mouse hepatic Stellate Cells (lipocyte), +631 CNhs13196- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13196/summary/coverage-.w5 768 384 1.0 sum 630 CAGE:Mouse hepatic Stellate Cells (lipocyte), +632 CNhs13197+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13197/summary/coverage+.w5 768 384 1.0 sum 633 CAGE:CD326+ enterocyte, pool2 +633 CNhs13197- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13197/summary/coverage-.w5 768 384 1.0 sum 632 CAGE:CD326+ enterocyte, pool2 +634 CNhs13199+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13199/summary/coverage+.w5 768 384 1.0 sum 635 CAGE:Ileum epithelium, pool1 +635 CNhs13199- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13199/summary/coverage-.w5 768 384 1.0 sum 634 CAGE:Ileum epithelium, pool1 +636 CNhs13200+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13200/summary/coverage+.w5 768 384 1.0 sum 637 CAGE:Follicle Associated Epithelium, pool3 +637 CNhs13200- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13200/summary/coverage-.w5 768 384 1.0 sum 636 CAGE:Follicle Associated Epithelium, pool3 +638 CNhs13214+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13201/summary/coverage+.w5 768 384 1.0 sum 639 CAGE:CD41+ megakaryocyte control, +639 CNhs13214- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13201/summary/coverage-.w5 768 384 1.0 sum 638 CAGE:CD41+ megakaryocyte control, +640 CNhs13209+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13209/summary/coverage+.w5 768 384 1.0 sum 641 CAGE:Mouse hepatic Sinusoidal Endothelial Cells, +641 CNhs13209- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13209/summary/coverage-.w5 768 384 1.0 sum 640 CAGE:Mouse hepatic Sinusoidal Endothelial Cells, +642 CNhs13210+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13210/summary/coverage+.w5 768 384 1.0 sum 643 CAGE:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool2 +643 CNhs13210- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13210/summary/coverage-.w5 768 384 1.0 sum 642 CAGE:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool2 +644 CNhs13211+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13211/summary/coverage+.w5 768 384 1.0 sum 645 CAGE:Follicle Associated Epithelium, pool2 +645 CNhs13211- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13211/summary/coverage-.w5 768 384 1.0 sum 644 CAGE:Follicle Associated Epithelium, pool2 +646 CNhs13217+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13217/summary/coverage+.w5 768 384 1.0 sum 647 CAGE:CD4+CD25-CD44- naive conventional T cells, pool1 (C57BL_6J) +647 CNhs13217- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13217/summary/coverage-.w5 768 384 1.0 sum 646 CAGE:CD4+CD25-CD44- naive conventional T cells, pool1 (C57BL_6J) +648 CNhs13218+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13218/summary/coverage+.w5 768 384 1.0 sum 649 CAGE:CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool1 (C57BL_6J) +649 CNhs13218- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13218/summary/coverage-.w5 768 384 1.0 sum 648 CAGE:CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool1 (C57BL_6J) +650 CNhs13219+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13219/summary/coverage+.w5 768 384 1.0 sum 651 CAGE:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool1 (C57BL_6J) +651 CNhs13219- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13219/summary/coverage-.w5 768 384 1.0 sum 650 CAGE:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool1 (C57BL_6J) +652 CNhs13220+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13220/summary/coverage+.w5 768 384 1.0 sum 653 CAGE:CD4+CD25-CD44- naive conventional T cells, pool2 (Balb_cAJcl) +653 CNhs13220- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13220/summary/coverage-.w5 768 384 1.0 sum 652 CAGE:CD4+CD25-CD44- naive conventional T cells, pool2 (Balb_cAJcl) +654 CNhs13221+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13221/summary/coverage+.w5 768 384 1.0 sum 655 CAGE:CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl) +655 CNhs13221- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13221/summary/coverage-.w5 768 384 1.0 sum 654 CAGE:CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl) +656 CNhs13225+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13225/summary/coverage+.w5 768 384 1.0 sum 657 CAGE:CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool2 (Balb_cAJcl) +657 CNhs13225- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13225/summary/coverage-.w5 768 384 1.0 sum 656 CAGE:CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool2 (Balb_cAJcl) +658 CNhs13226+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13226/summary/coverage+.w5 768 384 1.0 sum 659 CAGE:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl) +659 CNhs13226- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13226/summary/coverage-.w5 768 384 1.0 sum 658 CAGE:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl) +660 CNhs13228+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13228/summary/coverage+.w5 768 384 1.0 sum 661 CAGE:GP2+ M cell, pool1 +661 CNhs13228- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13228/summary/coverage-.w5 768 384 1.0 sum 660 CAGE:GP2+ M cell, pool1 +662 CNhs13231+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13231/summary/coverage+.w5 768 384 1.0 sum 663 CAGE:GP2+ M cell, pool2 +663 CNhs13231- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13231/summary/coverage-.w5 768 384 1.0 sum 662 CAGE:GP2+ M cell, pool2 +664 CNhs13232+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13232/summary/coverage+.w5 768 384 1.0 sum 665 CAGE:Ileum epithelium, pool2 +665 CNhs13232- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13232/summary/coverage-.w5 768 384 1.0 sum 664 CAGE:Ileum epithelium, pool2 +666 CNhs13233+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13233/summary/coverage+.w5 768 384 1.0 sum 667 CAGE:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool2 +667 CNhs13233- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13233/summary/coverage-.w5 768 384 1.0 sum 666 CAGE:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool2 +668 CNhs13236+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13236/summary/coverage+.w5 768 384 1.0 sum 669 CAGE:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool1 +669 CNhs13236- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13236/summary/coverage-.w5 768 384 1.0 sum 668 CAGE:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool1 +670 CNhs13240+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13240/summary/coverage+.w5 768 384 1.0 sum 671 CAGE:GP2+ M cell, pool3 +671 CNhs13240- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13240/summary/coverage-.w5 768 384 1.0 sum 670 CAGE:GP2+ M cell, pool3 +672 CNhs13242+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13242/summary/coverage+.w5 768 384 1.0 sum 673 CAGE:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool1 +673 CNhs13242- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13242/summary/coverage-.w5 768 384 1.0 sum 672 CAGE:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool1 +674 CNhs13509+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13509/summary/coverage+.w5 768 384 1.0 sum 675 CAGE:Mouse CD4+ T Cells, +675 CNhs13509- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13509/summary/coverage-.w5 768 384 1.0 sum 674 CAGE:Mouse CD4+ T Cells, +676 CNhs13511+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13511/summary/coverage+.w5 768 384 1.0 sum 677 CAGE:Mouse CD8+ T Cells, +677 CNhs13511- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13511/summary/coverage-.w5 768 384 1.0 sum 676 CAGE:Mouse CD8+ T Cells, +678 CNhs13531+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13531/summary/coverage+.w5 768 384 1.0 sum 679 CAGE:Mouse CD19+ B Cells, +679 CNhs13531- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13531/summary/coverage-.w5 768 384 1.0 sum 678 CAGE:Mouse CD19+ B Cells, +680 CNhs13542+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13542/summary/coverage+.w5 768 384 1.0 sum 681 CAGE:CD326+ enterocyte, pool1 +681 CNhs13542- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13542/summary/coverage-.w5 768 384 1.0 sum 680 CAGE:CD326+ enterocyte, pool1 +682 CNhs13913+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13913/summary/coverage+.w5 768 384 1.0 sum 683 CAGE:CD4+CD25+ regulatory T cells, pool1 (C57BL_6J) +683 CNhs13913- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs13913/summary/coverage-.w5 768 384 1.0 sum 682 CAGE:CD4+CD25+ regulatory T cells, pool1 (C57BL_6J) +684 CNhs14136+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14136/summary/coverage+.w5 768 384 1.0 sum 685 CAGE:macrophage, bone marrow derived +685 CNhs14136- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14136/summary/coverage-.w5 768 384 1.0 sum 684 CAGE:macrophage, bone marrow derived +686 CNhs14137+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14137/summary/coverage+.w5 768 384 1.0 sum 687 CAGE:osteoclast, bone marrow derived +687 CNhs14137- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14137/summary/coverage-.w5 768 384 1.0 sum 686 CAGE:osteoclast, bone marrow derived +688 CNhs14142+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14142/summary/coverage+.w5 768 384 1.0 sum 689 CAGE:CD4+CD25+ regulatory T cells, PMA and ionomycin stimulation, 02hr, pool1 (C57BL 6J) +689 CNhs14142- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14142/summary/coverage-.w5 768 384 1.0 sum 688 CAGE:CD4+CD25+ regulatory T cells, PMA and ionomycin stimulation, 02hr, pool1 (C57BL 6J) +690 CNhs14147+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14147/summary/coverage+.w5 768 384 1.0 sum 691 CAGE:Neurons - spiral ganglion, pool1 +691 CNhs14147- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14147/summary/coverage-.w5 768 384 1.0 sum 690 CAGE:Neurons - spiral ganglion, pool1 +692 CNhs14158+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14158/summary/coverage+.w5 768 384 1.0 sum 693 CAGE:CD4+CD25+ regulatory T cells, antiCD3 CD28 stimulation, 06hr, pool1 (BalbcA) +693 CNhs14158- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14158/summary/coverage-.w5 768 384 1.0 sum 692 CAGE:CD4+CD25+ regulatory T cells, antiCD3 CD28 stimulation, 06hr, pool1 (BalbcA) +694 CNhs14159+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14159/summary/coverage+.w5 768 384 1.0 sum 695 CAGE:CD4+CD25+ regulatory T cells, antiCD3 CD28 stimulation, 06hr, pool1 (C57BL 6J) +695 CNhs14159- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14159/summary/coverage-.w5 768 384 1.0 sum 694 CAGE:CD4+CD25+ regulatory T cells, antiCD3 CD28 stimulation, 06hr, pool1 (C57BL 6J) +696 CNhs14160+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14160/summary/coverage+.w5 768 384 1.0 sum 697 CAGE:CD4+CD25+ regulatory T cells, PMA and ionomycin stimulation, 02hr, pool1 (BalbcA) +697 CNhs14160- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14160/summary/coverage-.w5 768 384 1.0 sum 696 CAGE:CD4+CD25+ regulatory T cells, PMA and ionomycin stimulation, 02hr, pool1 (BalbcA) +698 CNhs14335+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14330/summary/coverage+.w5 768 384 1.0 sum 699 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_rep2 +699 CNhs14335- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14330/summary/coverage-.w5 768 384 1.0 sum 698 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_rep2 +700 CNhs14336+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14331/summary/coverage+.w5 768 384 1.0 sum 701 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_rep2 +701 CNhs14336- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14331/summary/coverage-.w5 768 384 1.0 sum 700 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_rep2 +702 CNhs14332+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14332/summary/coverage+.w5 768 384 1.0 sum 703 CAGE:natural helper cells, IL33 treated, 01hr, biol_, tech_rep2 +703 CNhs14332- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14332/summary/coverage-.w5 768 384 1.0 sum 702 CAGE:natural helper cells, IL33 treated, 01hr, biol_, tech_rep2 +704 CNhs14333+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14333/summary/coverage+.w5 768 384 1.0 sum 705 CAGE:natural helper cells, naive, biol_, tech_rep2 +705 CNhs14333- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14333/summary/coverage-.w5 768 384 1.0 sum 704 CAGE:natural helper cells, naive, biol_, tech_rep2 +706 CNhs14337+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14337/summary/coverage+.w5 768 384 1.0 sum 707 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_ +707 CNhs14337- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14337/summary/coverage-.w5 768 384 1.0 sum 706 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_ +708 CNhs14387+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14341/summary/coverage+.w5 768 384 1.0 sum 709 CAGE:natural helper cells, naive, biol_, tech_ +709 CNhs14387- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14341/summary/coverage-.w5 768 384 1.0 sum 708 CAGE:natural helper cells, naive, biol_, tech_ +710 CNhs14388+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14378/summary/coverage+.w5 768 384 1.0 sum 711 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_rep3 +711 CNhs14388- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14378/summary/coverage-.w5 768 384 1.0 sum 710 CAGE:natural helper cells, IL2 treated, day15, biol_, tech_rep3 +712 CNhs14382+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14381/summary/coverage+.w5 768 384 1.0 sum 713 CAGE:natural helper cells, naive, biol_, tech_rep3 +713 CNhs14382- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14381/summary/coverage-.w5 768 384 1.0 sum 712 CAGE:natural helper cells, naive, biol_, tech_rep3 +714 CNhs14383+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14383/summary/coverage+.w5 768 384 1.0 sum 715 CAGE:natural helper cells, IL33 treated, 01hr, biol_, tech_rep3 +715 CNhs14383- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14383/summary/coverage-.w5 768 384 1.0 sum 714 CAGE:natural helper cells, IL33 treated, 01hr, biol_, tech_rep3 +716 CNhs14386+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14385/summary/coverage+.w5 768 384 1.0 sum 717 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_rep3 +717 CNhs14386- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14385/summary/coverage-.w5 768 384 1.0 sum 716 CAGE:natural helper cells, IL33 treated, day02, biol_, tech_rep3 +718 CNhs14555+ /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14555/summary/coverage+.w5 768 384 1.0 sum 719 CAGE:Mouse Renal epithelial cells, +719 CNhs14555- /home/drk/tillage/datasets/mouse/cage/fantom/CNhs14555/summary/coverage-.w5 768 384 1.0 sum 718 CAGE:Mouse Renal epithelial cells, +720 GSM1437735 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437735/summary/coverage.w5 256 64 1.0 sum 720 GRO:GRO-seq WT Liver ZT1 / liver / . +721 GSM1437736 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437736/summary/coverage.w5 256 64 1.0 sum 721 GRO:GRO-seq WT Liver ZT4 / liver / . +722 GSM1437737 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437737/summary/coverage.w5 256 64 1.0 sum 722 GRO:GRO-seq WT Liver ZT7 / liver / . +723 GSM1437738 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437738/summary/coverage.w5 256 64 1.0 sum 723 GRO:GRO-seq WT Liver ZT10 / liver / . +724 GSM1437739 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437739/summary/coverage.w5 256 64 1.0 sum 724 GRO:GRO-seq WT Liver ZT13 / liver / . +725 GSM1437740 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437740/summary/coverage.w5 256 64 1.0 sum 725 GRO:GRO-seq WT LiverZT16 / liver / . +726 GSM1437741 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437741/summary/coverage.w5 256 64 1.0 sum 726 GRO:GRO-seq WT Liver ZT19 / liver / . +727 GSM1437742 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437742/summary/coverage.w5 256 64 1.0 sum 727 GRO:GRO-seq WT Liver ZT22 / liver / . +728 GSM1437745 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437745/summary/coverage.w5 256 64 1.0 sum 728 GRO:GRO-seq Rev-erbA WT Liver ZT10 / liver / . +729 GSM1437746 /home/drk/tillage/datasets/mouse/gro/geo/GSM1437746/summary/coverage.w5 256 64 1.0 sum 729 GRO:GRO-seq Rev-erbA KO Liver ZT10 / liver / . +730 ENCFF866ZTV /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMK/summary/coverage.w5 128 32 2.0 mean 730 DNASE:B6D2F1/J 416B +731 ENCFF695LHM /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CML/summary/coverage.w5 128 32 2.0 mean 731 DNASE:BALB/cAnN A20 +732 ENCFF079SPZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMM/summary/coverage.w5 128 32 2.0 mean 732 DNASE:C57BL/6 B cell male adult (8 weeks) +733 ENCFF798VSP /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMN/summary/coverage.w5 128 32 2.0 mean 733 DNASE:C57BL/6 splenic B cell male adult (8 weeks) +734 ENCFF474GND /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMO/summary/coverage.w5 128 32 2.0 mean 734 DNASE:C57BL/6 cerebellum male adult (8 weeks) +735 ENCFF395AJZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMP/summary/coverage.w5 128 32 2.0 mean 735 DNASE:C57BL/6 telencephalon male adult (8 weeks) +736 ENCFF990TBH /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMR/summary/coverage.w5 128 32 2.0 mean 736 DNASE:CD-1 c-Kit-negative CD71-positive TER-119-positive erythroid progenitor cells male embryo (14.5 days) +737 ENCFF443PWY /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMS/summary/coverage.w5 128 32 2.0 mean 737 DNASE:CD-1 c-Kit-positive CD71-negative TER-119-negative erythroid progenitor cells male embryo (14.5 days) +738 ENCFF680ZTZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMT/summary/coverage.w5 128 32 2.0 mean 738 DNASE:CD-1 c-Kit-positive CD71-positive TER-119-negative erythroid progenitor cells male embryo (14.5 days) +739 ENCFF649DYS /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMU/summary/coverage.w5 128 32 2.0 mean 739 DNASE:CD-1 c-Kit-positive CD71-positive TER-119-positive erythroid progenitor cells male embryo (14.5 days) +740 ENCFF680PQC /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMV/summary/coverage.w5 128 32 2.0 mean 740 DNASE:129 ES-CJ7 +741 ENCFF872IES /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMW/summary/coverage.w5 128 32 2.0 mean 741 DNASE:129 ES-E14 +742 ENCFF974BRL /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMX/summary/coverage.w5 128 32 2.0 mean 742 DNASE:mixed WW6 +743 ENCFF660XSJ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CMY/summary/coverage.w5 128 32 2.0 mean 743 DNASE:mixed WW6 +744 ENCFF391SPW /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNA/summary/coverage.w5 128 32 2.0 mean 744 DNASE:C57BL/6 fibroblast of lung male adult (8 weeks) +745 ENCFF837OUY /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNB/summary/coverage.w5 128 32 2.0 mean 745 DNASE:CD-1 forelimb bud male embryo (11.5 days) +746 ENCFF090NJT /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNC/summary/coverage.w5 128 32 2.0 mean 746 DNASE:C57BL/6 gonadal fat pad male adult (8 weeks) +747 ENCFF227XDD /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CND/summary/coverage.w5 128 32 2.0 mean 747 DNASE:CD-1 embryo male embryo (11.5 days) depleted in head +748 ENCFF773NKY /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNE/summary/coverage.w5 128 32 2.0 mean 748 DNASE:C57BL/6 heart male adult (8 weeks) +749 ENCFF037VPV /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNF/summary/coverage.w5 128 32 2.0 mean 749 DNASE:CD-1 hindlimb bud male embryo (11.5 days) +750 ENCFF561HSI /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNG/summary/coverage.w5 128 32 2.0 mean 750 DNASE:C57BL/6 kidney male adult (8 weeks) +751 ENCFF650OFZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNH/summary/coverage.w5 128 32 2.0 mean 751 DNASE:C57BL/6 large intestine male adult (8 weeks) +752 ENCFF395XSI /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNJ/summary/coverage.w5 128 32 2.0 mean 752 DNASE:C57BL/6 liver male embryo (14.5 days) +753 ENCFF906XJY /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNK/summary/coverage.w5 128 32 2.0 mean 753 DNASE:129 liver male embryo (14.5 days) +754 ENCFF435WED /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNL/summary/coverage.w5 128 32 2.0 mean 754 DNASE:129 liver male embryo (14.5 days) +755 ENCFF102MGA /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNM/summary/coverage.w5 128 32 2.0 mean 755 DNASE:C57BL/6 lung male adult (8 weeks) +756 ENCFF990ATO /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNN/summary/coverage.w5 128 32 2.0 mean 756 DNASE:DBA/2 MEL cell line +757 ENCFF673VVB /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNO/summary/coverage.w5 128 32 2.0 mean 757 DNASE:CD-1 mesoderm male embryo (11.5 days) +758 ENCFF223QRV /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNP/summary/coverage.w5 128 32 2.0 mean 758 DNASE:DBA/2 MEL-GATA-1-ER +759 ENCFF516XER /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNQ/summary/coverage.w5 128 32 2.0 mean 759 DNASE:DBA/2 erythroblast originated from MEL-GATA-1-ER treated with 1 uM estradiol for 24 hours +760 ENCFF178FCM /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNR/summary/coverage.w5 128 32 2.0 mean 760 DNASE:DBA/2 erythroblast originated from MEL-GATA-1-ER treated with 1 uM estradiol for 48 hours +761 ENCFF950ALJ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNS/summary/coverage.w5 128 32 2.0 mean 761 DNASE:NIH/Swiss NIH3T3 +762 ENCFF632WLC /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNT/summary/coverage.w5 128 32 2.0 mean 762 DNASE:M.spretus x C57BL/6J Patski +763 ENCFF908NIP /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNU/summary/coverage.w5 128 32 2.0 mean 763 DNASE:C57BL/6 retina male postnatal (7 days) +764 ENCFF261PZG /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNV/summary/coverage.w5 128 32 2.0 mean 764 DNASE:C57BL/6 retina male postnatal (1 day) +765 ENCFF259ZNG /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNW/summary/coverage.w5 128 32 2.0 mean 765 DNASE:C57BL/6 retina male adult (8 weeks) +766 ENCFF731YAA /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNX/summary/coverage.w5 128 32 2.0 mean 766 DNASE:C57BL/6 skeletal muscle tissue male adult (8 weeks) +767 ENCFF546FZT /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000CNY/summary/coverage.w5 128 32 2.0 mean 767 DNASE:C57BL/6 spleen male adult (8 weeks) +768 ENCFF896PZK /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COA/summary/coverage.w5 128 32 2.0 mean 768 DNASE:C57BL/6 CD4-positive helper T cell male adult (8 weeks) +769 ENCFF540HLI /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COB/summary/coverage.w5 128 32 2.0 mean 769 DNASE:C57BL/6 thymus male adult (8 weeks) +770 ENCFF242YCJ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COD/summary/coverage.w5 128 32 2.0 mean 770 DNASE:C57BL/6 induced T-regulatory cell male adult (8 weeks) +771 ENCFF992QCB /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COE/summary/coverage.w5 128 32 2.0 mean 771 DNASE:C57BL/6 brain male embryo (14.5 days) +772 ENCFF257BKZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COF/summary/coverage.w5 128 32 2.0 mean 772 DNASE:C57BL/6 brain male adult (8 weeks) +773 ENCFF333MPS /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COG/summary/coverage.w5 128 32 2.0 mean 773 DNASE:C57BL/6 brain male embryo (18.5 days) +774 ENCFF424XOH /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COH/summary/coverage.w5 128 32 2.0 mean 774 DNASE:129 ZHBTc4-mESC +775 ENCFF448ZJM /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COI/summary/coverage.w5 128 32 2.0 mean 775 DNASE:129 ZHBTc4-mESC treated with 100 ng/mL doxycycline hyclate for 24 hours +776 ENCFF825ZVT /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR000COJ/summary/coverage.w5 128 32 2.0 mean 776 DNASE:129 ZHBTc4-mESC treated with 100 ng/mL doxycycline hyclate for 6 hours +777 ENCFF513QAB /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR005WPU/summary/coverage.w5 128 32 2.0 mean 777 DNASE:C57BL/6 heart postnatal (0 days) +778 ENCFF009ALP /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR014SFF/summary/coverage.w5 128 32 2.0 mean 778 DNASE:C57BL/6 forebrain embryo (11.50 days) +779 ENCFF299KAN /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR066DPD/summary/coverage.w5 128 32 2.0 mean 779 DNASE:C57BL/6 kidney postnatal (0 days) +780 ENCFF417SAZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR094XAY/summary/coverage.w5 128 32 2.0 mean 780 DNASE:C57BL/6 lung postnatal (0 days) +781 ENCFF829UGS /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR172RHR/summary/coverage.w5 128 32 2.0 mean 781 DNASE:C57BL/6 embryo embryo (10.5 days) +782 ENCFF107NBQ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR179PIH/summary/coverage.w5 128 32 2.0 mean 782 DNASE:C57BL/6 hindbrain embryo (14.5 days) +783 ENCFF373NJX /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR196VDE/summary/coverage.w5 128 32 2.0 mean 783 DNASE:C57BL/6 embryonic facial prominence embryo (11.5 days) +784 ENCFF540VTK /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR216UMD/summary/coverage.w5 128 32 2.0 mean 784 DNASE:C57BL/6 liver postnatal (0 days) +785 ENCFF888LAZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR289BTM/summary/coverage.w5 128 32 2.0 mean 785 DNASE:C57BL/6 hindbrain embryo (10.50 days) +786 ENCFF906WCV /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR292QBA/summary/coverage.w5 128 32 2.0 mean 786 DNASE:C57BL/6 midbrain embryo (11.5 days) +787 ENCFF649UQO /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR312QVY/summary/coverage.w5 128 32 2.0 mean 787 DNASE:C57BL/6 neural tube embryo (11.5 days) +788 ENCFF729TAB /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR319PWR/summary/coverage.w5 128 32 2.0 mean 788 DNASE:C57BL/6 R1 +789 ENCFF149TTQ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR337EDG/summary/coverage.w5 128 32 2.0 mean 789 DNASE:C57BL/6 forebrain embryo (14.5 days) +790 ENCFF943PHW /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR358ESL/summary/coverage.w5 128 32 2.0 mean 790 DNASE:C57BL/6 hindbrain embryo (11.5 days) +791 ENCFF115OLL /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR367FCW/summary/coverage.w5 128 32 2.0 mean 791 DNASE:C57BL/6 midbrain embryo (14.5 days) +792 ENCFF963PGF /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR372SMH/summary/coverage.w5 128 32 2.0 mean 792 DNASE:DBA/2 MEL cell line treated with 125 uM zinc dichloride for 24 hours +793 ENCFF625SMQ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR380VCU/summary/coverage.w5 128 32 2.0 mean 793 DNASE:C57BL/6 limb embryo (10.50 days) +794 ENCFF155MQS /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR446MUM/summary/coverage.w5 128 32 2.0 mean 794 DNASE:DBA/2 MEL cell line +795 ENCFF283WGI /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR469VGZ/summary/coverage.w5 128 32 2.0 mean 795 DNASE:C57BL/6 hindbrain postnatal (0 days) +796 ENCFF266ZDD /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR488VEQ/summary/coverage.w5 128 32 2.0 mean 796 DNASE:C57BL/6 retina embryo (14.5 days) +797 ENCFF076VZF /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR561FZE/summary/coverage.w5 128 32 2.0 mean 797 DNASE:C57BL/6 liver embryo (11.50 days) +798 ENCFF802BPW /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR636NXY/summary/coverage.w5 128 32 2.0 mean 798 DNASE:C57BL/6 limb embryo (14.5 days) +799 ENCFF622EDP /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR655WKX/summary/coverage.w5 128 32 2.0 mean 799 DNASE:C57BL/6 intestine embryo (14.50 days) +800 ENCFF945EBN /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR661GMU/summary/coverage.w5 128 32 2.0 mean 800 DNASE:C57BL/6 neural tube embryo (10.50 days) +801 ENCFF641OPE /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR661HDP/summary/coverage.w5 128 32 2.0 mean 801 DNASE:C57BL/6 limb embryo (11.5 days) +802 ENCFF586XFN /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR666HFH/summary/coverage.w5 128 32 2.0 mean 802 DNASE:C57BL/6 Muller cell postnatal (12 days) +803 ENCFF435DKT /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR687EAW/summary/coverage.w5 128 32 2.0 mean 803 DNASE:C57BL/6 3T3-L1 +804 ENCFF363ULE /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR687JCD/summary/coverage.w5 128 32 2.0 mean 804 DNASE:C57BL/6 embryo embryo (9.50 days) +805 ENCFF894XDN /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR723IXU/summary/coverage.w5 128 32 2.0 mean 805 DNASE:C57BL/6 embryo embryo (10 days) +806 ENCFF919AUF /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR732IZK/summary/coverage.w5 128 32 2.0 mean 806 DNASE:C57BL/6 MN1 +807 ENCFF043UNG /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR742DUR/summary/coverage.w5 128 32 2.0 mean 807 DNASE:C57BL/6 lung embryo (14.5 days) +808 ENCFF071TLE /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR749ILN/summary/coverage.w5 128 32 2.0 mean 808 DNASE:C57BL/6 heart embryo (10.50 days) +809 ENCFF247KMU /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR756SPS/summary/coverage.w5 128 32 2.0 mean 809 DNASE:C57BL/6 forebrain embryo (10.50 days) +810 ENCFF610ONZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR767AJS/summary/coverage.w5 128 32 2.0 mean 810 DNASE:C57BL/6 midbrain postnatal (0 days) +811 ENCFF327SCP /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR773SAG/summary/coverage.w5 128 32 2.0 mean 811 DNASE:C57BL/6 midbrain embryo (10.50 days) +812 ENCFF846VXR /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR774TQO/summary/coverage.w5 128 32 2.0 mean 812 DNASE:C57BL/6 embryo embryo (11 day) +813 ENCFF458SNJ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR775YJL/summary/coverage.w5 128 32 2.0 mean 813 DNASE:C57BL/6 embryonic facial prominence embryo (10.50 days) +814 ENCFF684BQC /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR791AJY/summary/coverage.w5 128 32 2.0 mean 814 DNASE:C57BL/6 forebrain postnatal (0 days) +815 ENCFF014NWA /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR855ASN/summary/coverage.w5 128 32 2.0 mean 815 DNASE:C57BL/6 acute myeloid leukemia +816 ENCFF353HPD /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR894HWV/summary/coverage.w5 128 32 2.0 mean 816 DNASE:C57BL/6 yolk sac embryo (10.50 days) +817 ENCFF514HPX /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR898KAX/summary/coverage.w5 128 32 2.0 mean 817 DNASE:C57BL/6 MN1 treated with 10 nM methyltrienolone +818 ENCFF125IRZ /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR935RRY/summary/coverage.w5 128 32 2.0 mean 818 DNASE:C57BL/6 thymus postnatal (0 days) +819 ENCFF580UUE /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR959HKR/summary/coverage.w5 128 32 2.0 mean 819 DNASE:C57BL/6 embryonic facial prominence embryo (14.5 days) +820 ENCFF974HWL /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR964VDK/summary/coverage.w5 128 32 2.0 mean 820 DNASE:C57BL/6 R1 +821 ENCFF197TQR /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR969OPE/summary/coverage.w5 128 32 2.0 mean 821 DNASE:C57BL/6 stomach postnatal (0 days) +822 ENCFF325RFB /home/drk/tillage/datasets/mouse/dnase/encode/ENCSR998KYQ/summary/coverage.w5 128 32 2.0 mean 822 DNASE:C57BL/6 adipocyte +823 GSM1479701 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479701/summary/coverage.w5 256 64 1.0 sum 823 DNASE:DNase ZT 2 WT / Liver, WT, ZT 2, DNase / . +824 GSM1479702 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479702/summary/coverage.w5 256 64 1.0 sum 824 DNASE:DNase ZT 6 WT / Liver, WT, ZT 6, DNase / . +825 GSM1479703 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479703/summary/coverage.w5 256 64 1.0 sum 825 DNASE:DNase ZT 10 WT / Liver, WT, ZT 10, DNase / . +826 GSM1479704 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479704/summary/coverage.w5 256 64 1.0 sum 826 DNASE:DNase ZT 14 WT / Liver, WT, ZT 14, DNase / . +827 GSM1479705 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479705/summary/coverage.w5 256 64 1.0 sum 827 DNASE:DNase ZT 18 WT / Liver, WT, ZT 18, DNase / . +828 GSM1479706 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479706/summary/coverage.w5 256 64 1.0 sum 828 DNASE:DNase ZT 22 WT / Liver, WT, ZT 22, DNase / . +829 GSM1479707 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479707/summary/coverage.w5 256 64 1.0 sum 829 DNASE:DNase ZT 26 WT / Liver, WT, ZT 26, DNase / . +830 GSM1479708 /home/drk/tillage/datasets/mouse/dnase/geo/GSM1479708/summary/coverage.w5 256 64 1.0 sum 830 DNASE:DNase ZT 6 Bmal1 KO / Liver, Bmal1 KO, ZT 6, DNase / . +831 ENCFF745RFR /home/drk/tillage/datasets/mouse/atac/encode/ENCSR012YAB/summary/coverage.w5 128 32 2.0 mean 831 ATAC:C57BL/6 hindbrain embryo (11.5 days) +832 ENCFF446XWP /home/drk/tillage/datasets/mouse/atac/encode/ENCSR023QZX/summary/coverage.w5 128 32 2.0 mean 832 ATAC:C57BL/6 kidney embryo (15.5 days) +833 ENCFF700IKY /home/drk/tillage/datasets/mouse/atac/encode/ENCSR064IHX/summary/coverage.w5 128 32 2.0 mean 833 ATAC:C57BL/6 megakaryocyte-erythroid progenitor cell male adult (5-6 weeks) +834 ENCFF769BOR /home/drk/tillage/datasets/mouse/atac/encode/ENCSR079GOY/summary/coverage.w5 128 32 2.0 mean 834 ATAC:C57BL/6 intestine postnatal (0 days) +835 ENCFF860QUH /home/drk/tillage/datasets/mouse/atac/encode/ENCSR088UYE/summary/coverage.w5 128 32 2.0 mean 835 ATAC:C57BL/6 hindbrain embryo (12.5 days) +836 ENCFF242FBC /home/drk/tillage/datasets/mouse/atac/encode/ENCSR096JCC/summary/coverage.w5 128 32 2.0 mean 836 ATAC:C57BL/6 midbrain embryo (16.5 days) +837 ENCFF823RLW /home/drk/tillage/datasets/mouse/atac/encode/ENCSR102NGD/summary/coverage.w5 128 32 2.0 mean 837 ATAC:C57BL/6 lung postnatal (0 days) +838 ENCFF570DUW /home/drk/tillage/datasets/mouse/atac/encode/ENCSR136XSY/summary/coverage.w5 128 32 2.0 mean 838 ATAC:C57BL/6 erythroid progenitor cell male adult (5-6 weeks) +839 ENCFF321AYT /home/drk/tillage/datasets/mouse/atac/encode/ENCSR176BYZ/summary/coverage.w5 128 32 2.0 mean 839 ATAC:C57BL/6 hindbrain embryo (13.5 days) +840 ENCFF517RIA /home/drk/tillage/datasets/mouse/atac/encode/ENCSR229QKB/summary/coverage.w5 128 32 2.0 mean 840 ATAC:C57BL/6 megakaryocyte progenitor cell male adult (5-6 weeks) +841 ENCFF408OOS /home/drk/tillage/datasets/mouse/atac/encode/ENCSR257PGU/summary/coverage.w5 128 32 2.0 mean 841 ATAC:C57BL/6 granulocyte monocyte progenitor cell male adult (5-6 weeks) +842 ENCFF060HRT /home/drk/tillage/datasets/mouse/atac/encode/ENCSR273UFV/summary/coverage.w5 128 32 2.0 mean 842 ATAC:C57BL/6 forebrain embryo (11.5 days) +843 ENCFF731NRD /home/drk/tillage/datasets/mouse/atac/encode/ENCSR280ZDP/summary/coverage.w5 128 32 2.0 mean 843 ATAC:C57BL/6 G1E +844 ENCFF643SRL /home/drk/tillage/datasets/mouse/atac/encode/ENCSR302LIV/summary/coverage.w5 128 32 2.0 mean 844 ATAC:C57BL/6 liver embryo (12.5 days) +845 ENCFF092DWB /home/drk/tillage/datasets/mouse/atac/encode/ENCSR310MLB/summary/coverage.w5 128 32 2.0 mean 845 ATAC:C57BL/6 forebrain postnatal (0 days) +846 ENCFF609BWE /home/drk/tillage/datasets/mouse/atac/encode/ENCSR312LQX/summary/coverage.w5 128 32 2.0 mean 846 ATAC:C57BL/6 hindbrain postnatal (0 days) +847 ENCFF161EJL /home/drk/tillage/datasets/mouse/atac/encode/ENCSR351YUI/summary/coverage.w5 128 32 2.0 mean 847 ATAC:C57BL/6 neutrophil adult (5-6 weeks) +848 ENCFF683WEV /home/drk/tillage/datasets/mouse/atac/encode/ENCSR366VBB/summary/coverage.w5 128 32 2.0 mean 848 ATAC:C57BL/6 hematopoietic stem cell adult (5-6 weeks) +849 ENCFF889QAK /home/drk/tillage/datasets/mouse/atac/encode/ENCSR382RUC/summary/coverage.w5 128 32 2.0 mean 849 ATAC:C57BL/6 midbrain embryo (11.5 days) +850 ENCFF513ECX /home/drk/tillage/datasets/mouse/atac/encode/ENCSR428BSK/summary/coverage.w5 128 32 2.0 mean 850 ATAC:C57BL/6 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +851 ENCFF564GWQ /home/drk/tillage/datasets/mouse/atac/encode/ENCSR453AWR/summary/coverage.w5 128 32 2.0 mean 851 ATAC:C57BL/6 hematopoietic stem cell +852 ENCFF190LKP /home/drk/tillage/datasets/mouse/atac/encode/ENCSR468GUI/summary/coverage.w5 128 32 2.0 mean 852 ATAC:C57BL/6 midbrain embryo (15.5 days) +853 ENCFF047WUY /home/drk/tillage/datasets/mouse/atac/encode/ENCSR498DQA/summary/coverage.w5 128 32 2.0 mean 853 ATAC:C57BL/6 megakaryocyte male adult (5-6 weeks) +854 ENCFF329SPM /home/drk/tillage/datasets/mouse/atac/encode/ENCSR554JQP/summary/coverage.w5 128 32 2.0 mean 854 ATAC:C57BL/6 cerebellum adult +855 ENCFF917SGA /home/drk/tillage/datasets/mouse/atac/encode/ENCSR559FAJ/summary/coverage.w5 128 32 2.0 mean 855 ATAC:C57BL/6 forebrain embryo (12.5 days) +856 ENCFF238AZB /home/drk/tillage/datasets/mouse/atac/encode/ENCSR597BGP/summary/coverage.w5 128 32 2.0 mean 856 ATAC:C57BL/6 stomach postnatal (0 days) +857 ENCFF770CQD /home/drk/tillage/datasets/mouse/atac/encode/ENCSR609OHJ/summary/coverage.w5 128 32 2.0 mean 857 ATAC:C57BL/6 liver postnatal (0 days) +858 ENCFF956ZAH /home/drk/tillage/datasets/mouse/atac/encode/ENCSR623GSD/summary/coverage.w5 128 32 2.0 mean 858 ATAC:C57BL/6 hindbrain embryo (16.5 days) +859 ENCFF196PJB /home/drk/tillage/datasets/mouse/atac/encode/ENCSR732OTZ/summary/coverage.w5 128 32 2.0 mean 859 ATAC:C57BL/6 kidney embryo (16.5 days) +860 ENCFF331KWS /home/drk/tillage/datasets/mouse/atac/encode/ENCSR785NEL/summary/coverage.w5 128 32 2.0 mean 860 ATAC:C57BL/6 liver embryo (11.5 days) +861 ENCFF321OJD /home/drk/tillage/datasets/mouse/atac/encode/ENCSR793RAV/summary/coverage.w5 128 32 2.0 mean 861 ATAC:C57BL/6 erythroblast male adult (5-6 weeks) +862 ENCFF845NRJ /home/drk/tillage/datasets/mouse/atac/encode/ENCSR810HQR/summary/coverage.w5 128 32 2.0 mean 862 ATAC:C57BL/6 forebrain embryo (14.5 days) +863 ENCFF810TCB /home/drk/tillage/datasets/mouse/atac/encode/ENCSR819QOJ/summary/coverage.w5 128 32 2.0 mean 863 ATAC:C57BL/6 midbrain embryo (13.5 days) +864 ENCFF960LTM /home/drk/tillage/datasets/mouse/atac/encode/ENCSR836PUC/summary/coverage.w5 128 32 2.0 mean 864 ATAC:C57BL/6 forebrain embryo (16.5 days) +865 ENCFF320TGF /home/drk/tillage/datasets/mouse/atac/encode/ENCSR862JVD/summary/coverage.w5 128 32 2.0 mean 865 ATAC:C57BL/6 monocyte adult (5-6 weeks) +866 ENCFF878HWK /home/drk/tillage/datasets/mouse/atac/encode/ENCSR889WQX/summary/coverage.w5 128 32 2.0 mean 866 ATAC:C57BL/6 frontal cortex adult +867 ENCFF654YSF /home/drk/tillage/datasets/mouse/atac/encode/ENCSR903GMO/summary/coverage.w5 128 32 2.0 mean 867 ATAC:C57BL/6 forebrain embryo (13.5 days) +868 ENCFF705VCO /home/drk/tillage/datasets/mouse/atac/encode/ENCSR914PYX/summary/coverage.w5 128 32 2.0 mean 868 ATAC:C57BL/6 common myeloid progenitor male adult (5-6 weeks) +869 ENCFF114TFO /home/drk/tillage/datasets/mouse/atac/encode/ENCSR961SMM/summary/coverage.w5 128 32 2.0 mean 869 ATAC:C57BL/6 intestine embryo (15.5 days) +870 ENCFF258MGU /home/drk/tillage/datasets/mouse/atac/encode/ENCSR966ORC/summary/coverage.w5 128 32 2.0 mean 870 ATAC:C57BL/6 intestine embryo (16.5 days) +871 ENCFF487YTM /home/drk/tillage/datasets/mouse/atac/encode/ENCSR976LWP/summary/coverage.w5 128 32 2.0 mean 871 ATAC:C57BL/6 forebrain embryo (15.5 days) +872 ENCFF309CAW /home/drk/tillage/datasets/mouse/atac/encode/ENCSR983JWA/summary/coverage.w5 128 32 2.0 mean 872 ATAC:C57BL/6 neural tube embryo (15.5 days) +873 UW1.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW1.1/summary/Unknown-clusters_1-cluster_1_mm10.w5 128 32 4.0 mean 873 ATAC:Unknown-clusters_1-cluster_1 +874 UW1.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW1.2/summary/Unknown-clusters_1-cluster_2_mm10.w5 128 32 4.0 mean 874 ATAC:Unknown-clusters_1-cluster_2 +875 UW1.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW1.3/summary/Unknown-clusters_1-cluster_3_mm10.w5 128 32 4.0 mean 875 ATAC:Unknown-clusters_1-cluster_3 +876 UW10.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW10.1/summary/Hematopoietic_progenitors-clusters_10-cluster_1_mm10.w5 128 32 4.0 mean 876 ATAC:Hematopoietic_progenitors-clusters_10-cluster_1 +877 UW11.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW11.1/summary/Proximal_tubule-clusters_11-cluster_1_mm10.w5 128 32 4.0 mean 877 ATAC:Proximal_tubule-clusters_11-cluster_1 +878 UW11.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW11.2/summary/Proximal_tubule-clusters_11-cluster_2_mm10.w5 128 32 4.0 mean 878 ATAC:Proximal_tubule-clusters_11-cluster_2 +879 UW11.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW11.3/summary/Proximal_tubule-clusters_11-cluster_3_mm10.w5 128 32 4.0 mean 879 ATAC:Proximal_tubule-clusters_11-cluster_3 +880 UW11.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW11.4/summary/Proximal_tubule_S3-clusters_11-cluster_4_mm10.w5 128 32 4.0 mean 880 ATAC:Proximal_tubule_S3-clusters_11-cluster_4 +881 UW11.5 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW11.5/summary/Proximal_tubule-clusters_11-cluster_5_mm10.w5 128 32 4.0 mean 881 ATAC:Proximal_tubule-clusters_11-cluster_5 +882 UW12.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW12.1/summary/T_cells-clusters_12-cluster_1_mm10.w5 128 32 4.0 mean 882 ATAC:T_cells-clusters_12-cluster_1 +883 UW12.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW12.2/summary/Regulatory_T_cells-clusters_12-cluster_2_mm10.w5 128 32 4.0 mean 883 ATAC:Regulatory_T_cells-clusters_12-cluster_2 +884 UW12.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW12.3/summary/NK_cells-clusters_12-cluster_3_mm10.w5 128 32 4.0 mean 884 ATAC:NK_cells-clusters_12-cluster_3 +885 UW12.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW12.4/summary/T_cells-clusters_12-cluster_4_mm10.w5 128 32 4.0 mean 885 ATAC:T_cells-clusters_12-cluster_4 +886 UW12.5 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW12.5/summary/T_cells-clusters_12-cluster_5_mm10.w5 128 32 4.0 mean 886 ATAC:T_cells-clusters_12-cluster_5 +887 UW13.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW13.1/summary/Erythroblasts-clusters_13-cluster_1_mm10.w5 128 32 4.0 mean 887 ATAC:Erythroblasts-clusters_13-cluster_1 +888 UW14.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW14.1/summary/Sperm-clusters_14-cluster_1_mm10.w5 128 32 4.0 mean 888 ATAC:Sperm-clusters_14-cluster_1 +889 UW14.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW14.2/summary/Sperm-clusters_14-cluster_2_mm10.w5 128 32 4.0 mean 889 ATAC:Sperm-clusters_14-cluster_2 +890 UW14.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW14.3/summary/Sperm-clusters_14-cluster_3_mm10.w5 128 32 4.0 mean 890 ATAC:Sperm-clusters_14-cluster_3 +891 UW15.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW15.1/summary/Inhibitory_neurons-clusters_15-cluster_1_mm10.w5 128 32 4.0 mean 891 ATAC:Inhibitory_neurons-clusters_15-cluster_1 +892 UW15.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW15.2/summary/Inhibitory_neurons-clusters_15-cluster_2_mm10.w5 128 32 4.0 mean 892 ATAC:Inhibitory_neurons-clusters_15-cluster_2 +893 UW15.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW15.3/summary/SOM+_Interneurons-clusters_15-cluster_3_mm10.w5 128 32 4.0 mean 893 ATAC:SOM+_Interneurons-clusters_15-cluster_3 +894 UW16.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW16.1/summary/B_cells-clusters_16-cluster_1_mm10.w5 128 32 4.0 mean 894 ATAC:B_cells-clusters_16-cluster_1 +895 UW16.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW16.2/summary/Macrophages-clusters_16-cluster_2_mm10.w5 128 32 4.0 mean 895 ATAC:Macrophages-clusters_16-cluster_2 +896 UW16.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW16.3/summary/Microglia-clusters_16-cluster_3_mm10.w5 128 32 4.0 mean 896 ATAC:Microglia-clusters_16-cluster_3 +897 UW17.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW17.1/summary/Dendritic_cells-clusters_17-cluster_1_mm10.w5 128 32 4.0 mean 897 ATAC:Dendritic_cells-clusters_17-cluster_1 +898 UW17.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW17.2/summary/Alveolar_macrophages-clusters_17-cluster_2_mm10.w5 128 32 4.0 mean 898 ATAC:Alveolar_macrophages-clusters_17-cluster_2 +899 UW17.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW17.3/summary/Dendritic_cells-clusters_17-cluster_3_mm10.w5 128 32 4.0 mean 899 ATAC:Dendritic_cells-clusters_17-cluster_3 +900 UW17.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW17.4/summary/Collisions-clusters_17-cluster_4_mm10.w5 128 32 4.0 mean 900 ATAC:Collisions-clusters_17-cluster_4 +901 UW17.5 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW17.5/summary/Collisions-clusters_17-cluster_5_mm10.w5 128 32 4.0 mean 901 ATAC:Collisions-clusters_17-cluster_5 +902 UW18.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW18.1/summary/DCT_CD-clusters_18-cluster_1_mm10.w5 128 32 4.0 mean 902 ATAC:DCT_CD-clusters_18-cluster_1 +903 UW18.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW18.2/summary/Loop_of_henle-clusters_18-cluster_2_mm10.w5 128 32 4.0 mean 903 ATAC:Loop_of_henle-clusters_18-cluster_2 +904 UW18.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW18.3/summary/Loop_of_henle-clusters_18-cluster_3_mm10.w5 128 32 4.0 mean 904 ATAC:Loop_of_henle-clusters_18-cluster_3 +905 UW18.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW18.4/summary/Distal_convoluted_tubule-clusters_18-cluster_4_mm10.w5 128 32 4.0 mean 905 ATAC:Distal_convoluted_tubule-clusters_18-cluster_4 +906 UW18.5 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW18.5/summary/Collecting_duct-clusters_18-cluster_5_mm10.w5 128 32 4.0 mean 906 ATAC:Collecting_duct-clusters_18-cluster_5 +907 UW19.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW19.1/summary/Astrocytes-clusters_19-cluster_1_mm10.w5 128 32 4.0 mean 907 ATAC:Astrocytes-clusters_19-cluster_1 +908 UW19.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW19.2/summary/Astrocytes-clusters_19-cluster_2_mm10.w5 128 32 4.0 mean 908 ATAC:Astrocytes-clusters_19-cluster_2 +909 UW19.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW19.3/summary/Astrocytes-clusters_19-cluster_3_mm10.w5 128 32 4.0 mean 909 ATAC:Astrocytes-clusters_19-cluster_3 +910 UW19.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW19.4/summary/Astrocytes-clusters_19-cluster_4_mm10.w5 128 32 4.0 mean 910 ATAC:Astrocytes-clusters_19-cluster_4 +911 UW2.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW2.1/summary/T_cells-clusters_2-cluster_1_mm10.w5 128 32 4.0 mean 911 ATAC:T_cells-clusters_2-cluster_1 +912 UW20.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW20.1/summary/Type_I_pneumocytes-clusters_20-cluster_1_mm10.w5 128 32 4.0 mean 912 ATAC:Type_I_pneumocytes-clusters_20-cluster_1 +913 UW21.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW21.1/summary/Oligodendrocytes-clusters_21-cluster_1_mm10.w5 128 32 4.0 mean 913 ATAC:Oligodendrocytes-clusters_21-cluster_1 +914 UW21.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW21.2/summary/Oligodendrocytes-clusters_21-cluster_2_mm10.w5 128 32 4.0 mean 914 ATAC:Oligodendrocytes-clusters_21-cluster_2 +915 UW22.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW22.1/summary/Endothelial_I_cells-clusters_22-cluster_1_mm10.w5 128 32 4.0 mean 915 ATAC:Endothelial_I_cells-clusters_22-cluster_1 +916 UW22.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW22.2/summary/Endothelial_I_glomerular-clusters_22-cluster_2_mm10.w5 128 32 4.0 mean 916 ATAC:Endothelial_I_(glomerular)-clusters_22-cluster_2 +917 UW22.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW22.3/summary/Endothelial_I_cells-clusters_22-cluster_3_mm10.w5 128 32 4.0 mean 917 ATAC:Endothelial_I_cells-clusters_22-cluster_3 +918 UW22.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW22.4/summary/Endothelial_I_cells-clusters_22-cluster_4_mm10.w5 128 32 4.0 mean 918 ATAC:Endothelial_I_cells-clusters_22-cluster_4 +919 UW23.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW23.1/summary/Endothelial_II_cells-clusters_23-cluster_1_mm10.w5 128 32 4.0 mean 919 ATAC:Endothelial_II_cells-clusters_23-cluster_1 +920 UW23.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW23.2/summary/Unknown-clusters_23-cluster_2_mm10.w5 128 32 4.0 mean 920 ATAC:Unknown-clusters_23-cluster_2 +921 UW24.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW24.1/summary/Monocytes-clusters_24-cluster_1_mm10.w5 128 32 4.0 mean 921 ATAC:Monocytes-clusters_24-cluster_1 +922 UW24.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW24.2/summary/Monocytes-clusters_24-cluster_2_mm10.w5 128 32 4.0 mean 922 ATAC:Monocytes-clusters_24-cluster_2 +923 UW25.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW25.1/summary/Podocytes-clusters_25-cluster_1_mm10.w5 128 32 4.0 mean 923 ATAC:Podocytes-clusters_25-cluster_1 +924 UW25.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW25.2/summary/Endothelial_II_cells-clusters_25-cluster_2_mm10.w5 128 32 4.0 mean 924 ATAC:Endothelial_II_cells-clusters_25-cluster_2 +925 UW25.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW25.3/summary/Endothelial_II_cells-clusters_25-cluster_3_mm10.w5 128 32 4.0 mean 925 ATAC:Endothelial_II_cells-clusters_25-cluster_3 +926 UW26.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW26.1/summary/T_cells-clusters_26-cluster_1_mm10.w5 128 32 4.0 mean 926 ATAC:T_cells-clusters_26-cluster_1 +927 UW26.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW26.2/summary/Collisions-clusters_26-cluster_2_mm10.w5 128 32 4.0 mean 927 ATAC:Collisions-clusters_26-cluster_2 +928 UW26.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW26.3/summary/Collisions-clusters_26-cluster_3_mm10.w5 128 32 4.0 mean 928 ATAC:Collisions-clusters_26-cluster_3 +929 UW27.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW27.1/summary/Purkinje_cells-clusters_27-cluster_1_mm10.w5 128 32 4.0 mean 929 ATAC:Purkinje_cells-clusters_27-cluster_1 +930 UW27.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW27.2/summary/Collisions-clusters_27-cluster_2_mm10.w5 128 32 4.0 mean 930 ATAC:Collisions-clusters_27-cluster_2 +931 UW27.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW27.3/summary/Collisions-clusters_27-cluster_3_mm10.w5 128 32 4.0 mean 931 ATAC:Collisions-clusters_27-cluster_3 +932 UW28.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW28.1/summary/Immature_B_cells-clusters_28-cluster_1_mm10.w5 128 32 4.0 mean 932 ATAC:Immature_B_cells-clusters_28-cluster_1 +933 UW28.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW28.2/summary/Immature_B_cells-clusters_28-cluster_2_mm10.w5 128 32 4.0 mean 933 ATAC:Immature_B_cells-clusters_28-cluster_2 +934 UW29.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW29.1/summary/Ex_neurons_SCPN-clusters_29-cluster_1_mm10.w5 128 32 4.0 mean 934 ATAC:Ex_neurons_SCPN-clusters_29-cluster_1 +935 UW3.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW3.1/summary/Hepatocytes-clusters_3-cluster_1_mm10.w5 128 32 4.0 mean 935 ATAC:Hepatocytes-clusters_3-cluster_1 +936 UW30.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW30.1/summary/Type_II_pneumocytes-clusters_30-cluster_1_mm10.w5 128 32 4.0 mean 936 ATAC:Type_II_pneumocytes-clusters_30-cluster_1 +937 UW30.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW30.2/summary/Unknown-clusters_30-cluster_2_mm10.w5 128 32 4.0 mean 937 ATAC:Unknown-clusters_30-cluster_2 +938 UW30.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW30.3/summary/Collisions-clusters_30-cluster_3_mm10.w5 128 32 4.0 mean 938 ATAC:Collisions-clusters_30-cluster_3 +939 UW30.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW30.4/summary/Unknown-clusters_30-cluster_4_mm10.w5 128 32 4.0 mean 939 ATAC:Unknown-clusters_30-cluster_4 +940 UW4.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW4.1/summary/B_cells-clusters_4-cluster_1_mm10.w5 128 32 4.0 mean 940 ATAC:B_cells-clusters_4-cluster_1 +941 UW4.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW4.2/summary/B_cells-clusters_4-cluster_2_mm10.w5 128 32 4.0 mean 941 ATAC:B_cells-clusters_4-cluster_2 +942 UW4.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW4.3/summary/B_cells-clusters_4-cluster_3_mm10.w5 128 32 4.0 mean 942 ATAC:B_cells-clusters_4-cluster_3 +943 UW4.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW4.4/summary/Activated_B_cells-clusters_4-cluster_4_mm10.w5 128 32 4.0 mean 943 ATAC:Activated_B_cells-clusters_4-cluster_4 +944 UW5.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW5.1/summary/Ex_neurons_CPN-clusters_5-cluster_1_mm10.w5 128 32 4.0 mean 944 ATAC:Ex_neurons_CPN-clusters_5-cluster_1 +945 UW5.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW5.2/summary/Ex_neurons_SCPN-clusters_5-cluster_2_mm10.w5 128 32 4.0 mean 945 ATAC:Ex_neurons_SCPN-clusters_5-cluster_2 +946 UW5.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW5.3/summary/Ex_neurons_CThPN-clusters_5-cluster_3_mm10.w5 128 32 4.0 mean 946 ATAC:Ex_neurons_CThPN-clusters_5-cluster_3 +947 UW5.4 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW5.4/summary/Ex_neurons_CThPN-clusters_5-cluster_4_mm10.w5 128 32 4.0 mean 947 ATAC:Ex_neurons_CThPN-clusters_5-cluster_4 +948 UW5.5 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW5.5/summary/Inhibitory_neurons-clusters_5-cluster_5_mm10.w5 128 32 4.0 mean 948 ATAC:Inhibitory_neurons-clusters_5-cluster_5 +949 UW5.6 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW5.6/summary/Unknown-clusters_5-cluster_6_mm10.w5 128 32 4.0 mean 949 ATAC:Unknown-clusters_5-cluster_6 +950 UW6.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW6.1/summary/Enterocytes-clusters_6-cluster_1_mm10.w5 128 32 4.0 mean 950 ATAC:Enterocytes-clusters_6-cluster_1 +951 UW7.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW7.1/summary/Cardiomyocytes-clusters_7-cluster_1_mm10.w5 128 32 4.0 mean 951 ATAC:Cardiomyocytes-clusters_7-cluster_1 +952 UW7.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW7.2/summary/Unknown-clusters_7-cluster_2_mm10.w5 128 32 4.0 mean 952 ATAC:Unknown-clusters_7-cluster_2 +953 UW8.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW8.1/summary/Cerebellar_granule_cells-clusters_8-cluster_1_mm10.w5 128 32 4.0 mean 953 ATAC:Cerebellar_granule_cells-clusters_8-cluster_1 +954 UW8.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW8.2/summary/Cerebellar_granule_cells-clusters_8-cluster_2_mm10.w5 128 32 4.0 mean 954 ATAC:Cerebellar_granule_cells-clusters_8-cluster_2 +955 UW9.1 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW9.1/summary/Unknown-clusters_9-cluster_1_mm10.w5 128 32 4.0 mean 955 ATAC:Unknown-clusters_9-cluster_1 +956 UW9.2 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW9.2/summary/Endothelial_II_cells-clusters_9-cluster_2_mm10.w5 128 32 4.0 mean 956 ATAC:Endothelial_II_cells-clusters_9-cluster_2 +957 UW9.3 /home/drk/tillage/datasets/mouse/atac/uw-atlas/UW9.3/summary/Endothelial_II_cells-clusters_9-cluster_3_mm10.w5 128 32 4.0 mean 957 ATAC:Endothelial_II_cells-clusters_9-cluster_3 +958 yangli1 /home/drk/tillage/datasets/mouse/atac/catlas/yangli1/summary/ASCG.w5 384 96 0.01 sum 958 ATAC:ASCG +959 yangli10 /home/drk/tillage/datasets/mouse/atac/catlas/yangli10/summary/CA3GL4.w5 384 96 0.01 sum 959 ATAC:CA3GL4 +960 yangli100 /home/drk/tillage/datasets/mouse/atac/catlas/yangli100/summary/OBGL1.w5 384 96 0.01 sum 960 ATAC:OBGL1 +961 yangli101 /home/drk/tillage/datasets/mouse/atac/catlas/yangli101/summary/OBGL2.w5 384 96 0.01 sum 961 ATAC:OBGL2 +962 yangli102 /home/drk/tillage/datasets/mouse/atac/catlas/yangli102/summary/OBGL3.w5 384 96 0.01 sum 962 ATAC:OBGL3 +963 yangli103 /home/drk/tillage/datasets/mouse/atac/catlas/yangli103/summary/OBGL4.w5 384 96 0.01 sum 963 ATAC:OBGL4 +964 yangli104 /home/drk/tillage/datasets/mouse/atac/catlas/yangli104/summary/OBGL5.w5 384 96 0.01 sum 964 ATAC:OBGL5 +965 yangli105 /home/drk/tillage/datasets/mouse/atac/catlas/yangli105/summary/OBNBL.w5 384 96 0.01 sum 965 ATAC:OBNBL +966 yangli106 /home/drk/tillage/datasets/mouse/atac/catlas/yangli106/summary/OLFGL1.w5 384 96 0.01 sum 966 ATAC:OLFGL1 +967 yangli107 /home/drk/tillage/datasets/mouse/atac/catlas/yangli107/summary/OLFGL2.w5 384 96 0.01 sum 967 ATAC:OLFGL2 +968 yangli108 /home/drk/tillage/datasets/mouse/atac/catlas/yangli108/summary/OLFGL3.w5 384 96 0.01 sum 968 ATAC:OLFGL3 +969 yangli109 /home/drk/tillage/datasets/mouse/atac/catlas/yangli109/summary/OLFGL4.w5 384 96 0.01 sum 969 ATAC:OLFGL4 +970 yangli11 /home/drk/tillage/datasets/mouse/atac/catlas/yangli11/summary/CA3GL5.w5 384 96 0.01 sum 970 ATAC:CA3GL5 +971 yangli110 /home/drk/tillage/datasets/mouse/atac/catlas/yangli110/summary/OLFGL5.w5 384 96 0.01 sum 971 ATAC:OLFGL5 +972 yangli111 /home/drk/tillage/datasets/mouse/atac/catlas/yangli111/summary/OLFGL6.w5 384 96 0.01 sum 972 ATAC:OLFGL6 +973 yangli112 /home/drk/tillage/datasets/mouse/atac/catlas/yangli112/summary/OLFGL7.w5 384 96 0.01 sum 973 ATAC:OLFGL7 +974 yangli113 /home/drk/tillage/datasets/mouse/atac/catlas/yangli113/summary/OPC.w5 384 96 0.01 sum 974 ATAC:OPC +975 yangli114 /home/drk/tillage/datasets/mouse/atac/catlas/yangli114/summary/PER.w5 384 96 0.01 sum 975 ATAC:PER +976 yangli115 /home/drk/tillage/datasets/mouse/atac/catlas/yangli115/summary/PIRGL.w5 384 96 0.01 sum 976 ATAC:PIRGL +977 yangli116 /home/drk/tillage/datasets/mouse/atac/catlas/yangli116/summary/PTGL1.w5 384 96 0.01 sum 977 ATAC:PTGL1 +978 yangli117 /home/drk/tillage/datasets/mouse/atac/catlas/yangli117/summary/PTGL2.w5 384 96 0.01 sum 978 ATAC:PTGL2 +979 yangli118 /home/drk/tillage/datasets/mouse/atac/catlas/yangli118/summary/PTGL3.w5 384 96 0.01 sum 979 ATAC:PTGL3 +980 yangli119 /home/drk/tillage/datasets/mouse/atac/catlas/yangli119/summary/PTGL4.w5 384 96 0.01 sum 980 ATAC:PTGL4 +981 yangli12 /home/drk/tillage/datasets/mouse/atac/catlas/yangli12/summary/CA3GL6.w5 384 96 0.01 sum 981 ATAC:CA3GL6 +982 yangli120 /home/drk/tillage/datasets/mouse/atac/catlas/yangli120/summary/PTGL5.w5 384 96 0.01 sum 982 ATAC:PTGL5 +983 yangli121 /home/drk/tillage/datasets/mouse/atac/catlas/yangli121/summary/PTGL6.w5 384 96 0.01 sum 983 ATAC:PTGL6 +984 yangli122 /home/drk/tillage/datasets/mouse/atac/catlas/yangli122/summary/PTGL7.w5 384 96 0.01 sum 984 ATAC:PTGL7 +985 yangli123 /home/drk/tillage/datasets/mouse/atac/catlas/yangli123/summary/PTGL8.w5 384 96 0.01 sum 985 ATAC:PTGL8 +986 yangli124 /home/drk/tillage/datasets/mouse/atac/catlas/yangli124/summary/PVGA1.w5 384 96 0.01 sum 986 ATAC:PVGA1 +987 yangli125 /home/drk/tillage/datasets/mouse/atac/catlas/yangli125/summary/PVGA2.w5 384 96 0.01 sum 987 ATAC:PVGA2 +988 yangli126 /home/drk/tillage/datasets/mouse/atac/catlas/yangli126/summary/PVGA3.w5 384 96 0.01 sum 988 ATAC:PVGA3 +989 yangli127 /home/drk/tillage/datasets/mouse/atac/catlas/yangli127/summary/PVGA4.w5 384 96 0.01 sum 989 ATAC:PVGA4 +990 yangli128 /home/drk/tillage/datasets/mouse/atac/catlas/yangli128/summary/PVGA5.w5 384 96 0.01 sum 990 ATAC:PVGA5 +991 yangli129 /home/drk/tillage/datasets/mouse/atac/catlas/yangli129/summary/PVGA6.w5 384 96 0.01 sum 991 ATAC:PVGA6 +992 yangli13 /home/drk/tillage/datasets/mouse/atac/catlas/yangli13/summary/CLAGL1.w5 384 96 0.01 sum 992 ATAC:CLAGL1 +993 yangli130 /home/drk/tillage/datasets/mouse/atac/catlas/yangli130/summary/PVGA7.w5 384 96 0.01 sum 993 ATAC:PVGA7 +994 yangli131 /home/drk/tillage/datasets/mouse/atac/catlas/yangli131/summary/PVM.w5 384 96 0.01 sum 994 ATAC:PVM +995 yangli132 /home/drk/tillage/datasets/mouse/atac/catlas/yangli132/summary/RGDG.w5 384 96 0.01 sum 995 ATAC:RGDG +996 yangli133 /home/drk/tillage/datasets/mouse/atac/catlas/yangli133/summary/RGSZ.w5 384 96 0.01 sum 996 ATAC:RGSZ +997 yangli134 /home/drk/tillage/datasets/mouse/atac/catlas/yangli134/summary/SSTGA1.w5 384 96 0.01 sum 997 ATAC:SSTGA1 +998 yangli135 /home/drk/tillage/datasets/mouse/atac/catlas/yangli135/summary/SSTGA10.w5 384 96 0.01 sum 998 ATAC:SSTGA10 +999 yangli136 /home/drk/tillage/datasets/mouse/atac/catlas/yangli136/summary/SSTGA2.w5 384 96 0.01 sum 999 ATAC:SSTGA2 +1000 yangli137 /home/drk/tillage/datasets/mouse/atac/catlas/yangli137/summary/SSTGA3.w5 384 96 0.01 sum 1000 ATAC:SSTGA3 +1001 yangli138 /home/drk/tillage/datasets/mouse/atac/catlas/yangli138/summary/SSTGA4.w5 384 96 0.01 sum 1001 ATAC:SSTGA4 +1002 yangli139 /home/drk/tillage/datasets/mouse/atac/catlas/yangli139/summary/SSTGA5.w5 384 96 0.01 sum 1002 ATAC:SSTGA5 +1003 yangli14 /home/drk/tillage/datasets/mouse/atac/catlas/yangli14/summary/CLAGL2.w5 384 96 0.01 sum 1003 ATAC:CLAGL2 +1004 yangli140 /home/drk/tillage/datasets/mouse/atac/catlas/yangli140/summary/SSTGA6.w5 384 96 0.01 sum 1004 ATAC:SSTGA6 +1005 yangli141 /home/drk/tillage/datasets/mouse/atac/catlas/yangli141/summary/SSTGA7.w5 384 96 0.01 sum 1005 ATAC:SSTGA7 +1006 yangli142 /home/drk/tillage/datasets/mouse/atac/catlas/yangli142/summary/SSTGA8.w5 384 96 0.01 sum 1006 ATAC:SSTGA8 +1007 yangli143 /home/drk/tillage/datasets/mouse/atac/catlas/yangli143/summary/SSTGA9.w5 384 96 0.01 sum 1007 ATAC:SSTGA9 +1008 yangli144 /home/drk/tillage/datasets/mouse/atac/catlas/yangli144/summary/STRGA1.w5 384 96 0.01 sum 1008 ATAC:STRGA1 +1009 yangli145 /home/drk/tillage/datasets/mouse/atac/catlas/yangli145/summary/STRGA2.w5 384 96 0.01 sum 1009 ATAC:STRGA2 +1010 yangli146 /home/drk/tillage/datasets/mouse/atac/catlas/yangli146/summary/STRGA3.w5 384 96 0.01 sum 1010 ATAC:STRGA3 +1011 yangli147 /home/drk/tillage/datasets/mouse/atac/catlas/yangli147/summary/STRGA4.w5 384 96 0.01 sum 1011 ATAC:STRGA4 +1012 yangli148 /home/drk/tillage/datasets/mouse/atac/catlas/yangli148/summary/STRGA5.w5 384 96 0.01 sum 1012 ATAC:STRGA5 +1013 yangli149 /home/drk/tillage/datasets/mouse/atac/catlas/yangli149/summary/STRGA6.w5 384 96 0.01 sum 1013 ATAC:STRGA6 +1014 yangli15 /home/drk/tillage/datasets/mouse/atac/catlas/yangli15/summary/CLAGL3.w5 384 96 0.01 sum 1014 ATAC:CLAGL3 +1015 yangli150 /home/drk/tillage/datasets/mouse/atac/catlas/yangli150/summary/VEC.w5 384 96 0.01 sum 1015 ATAC:VEC +1016 yangli151 /home/drk/tillage/datasets/mouse/atac/catlas/yangli151/summary/VIPGA1.w5 384 96 0.01 sum 1016 ATAC:VIPGA1 +1017 yangli152 /home/drk/tillage/datasets/mouse/atac/catlas/yangli152/summary/VIPGA2.w5 384 96 0.01 sum 1017 ATAC:VIPGA2 +1018 yangli153 /home/drk/tillage/datasets/mouse/atac/catlas/yangli153/summary/VIPGA3.w5 384 96 0.01 sum 1018 ATAC:VIPGA3 +1019 yangli154 /home/drk/tillage/datasets/mouse/atac/catlas/yangli154/summary/VIPGA4.w5 384 96 0.01 sum 1019 ATAC:VIPGA4 +1020 yangli155 /home/drk/tillage/datasets/mouse/atac/catlas/yangli155/summary/VLMC1.w5 384 96 0.01 sum 1020 ATAC:VLMC1 +1021 yangli156 /home/drk/tillage/datasets/mouse/atac/catlas/yangli156/summary/VLMC2.w5 384 96 0.01 sum 1021 ATAC:VLMC2 +1022 yangli157 /home/drk/tillage/datasets/mouse/atac/catlas/yangli157/summary/VLMC3.w5 384 96 0.01 sum 1022 ATAC:VLMC3 +1023 yangli158 /home/drk/tillage/datasets/mouse/atac/catlas/yangli158/summary/VPIA1.w5 384 96 0.01 sum 1023 ATAC:VPIA1 +1024 yangli159 /home/drk/tillage/datasets/mouse/atac/catlas/yangli159/summary/VPIA2.w5 384 96 0.01 sum 1024 ATAC:VPIA2 +1025 yangli16 /home/drk/tillage/datasets/mouse/atac/catlas/yangli16/summary/CNUGA.w5 384 96 0.01 sum 1025 ATAC:CNUGA +1026 yangli160 /home/drk/tillage/datasets/mouse/atac/catlas/yangli160/summary/VPIA3.w5 384 96 0.01 sum 1026 ATAC:VPIA3 +1027 yangli17 /home/drk/tillage/datasets/mouse/atac/catlas/yangli17/summary/COP.w5 384 96 0.01 sum 1027 ATAC:COP +1028 yangli18 /home/drk/tillage/datasets/mouse/atac/catlas/yangli18/summary/CRC.w5 384 96 0.01 sum 1028 ATAC:CRC +1029 yangli19 /home/drk/tillage/datasets/mouse/atac/catlas/yangli19/summary/CTGL1.w5 384 96 0.01 sum 1029 ATAC:CTGL1 +1030 yangli2 /home/drk/tillage/datasets/mouse/atac/catlas/yangli2/summary/ASCN.w5 384 96 0.01 sum 1030 ATAC:ASCN +1031 yangli20 /home/drk/tillage/datasets/mouse/atac/catlas/yangli20/summary/CTGL2.w5 384 96 0.01 sum 1031 ATAC:CTGL2 +1032 yangli21 /home/drk/tillage/datasets/mouse/atac/catlas/yangli21/summary/CTGL3.w5 384 96 0.01 sum 1032 ATAC:CTGL3 +1033 yangli22 /home/drk/tillage/datasets/mouse/atac/catlas/yangli22/summary/CTGL4.w5 384 96 0.01 sum 1033 ATAC:CTGL4 +1034 yangli23 /home/drk/tillage/datasets/mouse/atac/catlas/yangli23/summary/CTGL5.w5 384 96 0.01 sum 1034 ATAC:CTGL5 +1035 yangli24 /home/drk/tillage/datasets/mouse/atac/catlas/yangli24/summary/CTGL6.w5 384 96 0.01 sum 1035 ATAC:CTGL6 +1036 yangli25 /home/drk/tillage/datasets/mouse/atac/catlas/yangli25/summary/D1MSN1.w5 384 96 0.01 sum 1036 ATAC:D1MSN1 +1037 yangli26 /home/drk/tillage/datasets/mouse/atac/catlas/yangli26/summary/D1MSN2.w5 384 96 0.01 sum 1037 ATAC:D1MSN2 +1038 yangli27 /home/drk/tillage/datasets/mouse/atac/catlas/yangli27/summary/D1MSN3.w5 384 96 0.01 sum 1038 ATAC:D1MSN3 +1039 yangli28 /home/drk/tillage/datasets/mouse/atac/catlas/yangli28/summary/D1MSN4.w5 384 96 0.01 sum 1039 ATAC:D1MSN4 +1040 yangli29 /home/drk/tillage/datasets/mouse/atac/catlas/yangli29/summary/D1MSN5.w5 384 96 0.01 sum 1040 ATAC:D1MSN5 +1041 yangli3 /home/drk/tillage/datasets/mouse/atac/catlas/yangli3/summary/ASCW.w5 384 96 0.01 sum 1041 ATAC:ASCW +1042 yangli30 /home/drk/tillage/datasets/mouse/atac/catlas/yangli30/summary/D2MSN1.w5 384 96 0.01 sum 1042 ATAC:D2MSN1 +1043 yangli31 /home/drk/tillage/datasets/mouse/atac/catlas/yangli31/summary/D2MSN2.w5 384 96 0.01 sum 1043 ATAC:D2MSN2 +1044 yangli32 /home/drk/tillage/datasets/mouse/atac/catlas/yangli32/summary/D2MSN3.w5 384 96 0.01 sum 1044 ATAC:D2MSN3 +1045 yangli33 /home/drk/tillage/datasets/mouse/atac/catlas/yangli33/summary/D2MSN4.w5 384 96 0.01 sum 1045 ATAC:D2MSN4 +1046 yangli34 /home/drk/tillage/datasets/mouse/atac/catlas/yangli34/summary/DGGR.w5 384 96 0.01 sum 1046 ATAC:DGGR +1047 yangli35 /home/drk/tillage/datasets/mouse/atac/catlas/yangli35/summary/DGNBL1.w5 384 96 0.01 sum 1047 ATAC:DGNBL1 +1048 yangli36 /home/drk/tillage/datasets/mouse/atac/catlas/yangli36/summary/DGNBL2.w5 384 96 0.01 sum 1048 ATAC:DGNBL2 +1049 yangli37 /home/drk/tillage/datasets/mouse/atac/catlas/yangli37/summary/DGNBL3.w5 384 96 0.01 sum 1049 ATAC:DGNBL3 +1050 yangli38 /home/drk/tillage/datasets/mouse/atac/catlas/yangli38/summary/ITHGL1.w5 384 96 0.01 sum 1050 ATAC:ITHGL1 +1051 yangli39 /home/drk/tillage/datasets/mouse/atac/catlas/yangli39/summary/ITHGL2.w5 384 96 0.01 sum 1051 ATAC:ITHGL2 +1052 yangli4 /home/drk/tillage/datasets/mouse/atac/catlas/yangli4/summary/CA1GL1.w5 384 96 0.01 sum 1052 ATAC:CA1GL1 +1053 yangli40 /home/drk/tillage/datasets/mouse/atac/catlas/yangli40/summary/ITHGL3.w5 384 96 0.01 sum 1053 ATAC:ITHGL3 +1054 yangli41 /home/drk/tillage/datasets/mouse/atac/catlas/yangli41/summary/ITL23GL1.w5 384 96 0.01 sum 1054 ATAC:ITL23GL1 +1055 yangli42 /home/drk/tillage/datasets/mouse/atac/catlas/yangli42/summary/ITL23GL2.w5 384 96 0.01 sum 1055 ATAC:ITL23GL2 +1056 yangli43 /home/drk/tillage/datasets/mouse/atac/catlas/yangli43/summary/ITL23GL3.w5 384 96 0.01 sum 1056 ATAC:ITL23GL3 +1057 yangli44 /home/drk/tillage/datasets/mouse/atac/catlas/yangli44/summary/ITL4GL1.w5 384 96 0.01 sum 1057 ATAC:ITL4GL1 +1058 yangli45 /home/drk/tillage/datasets/mouse/atac/catlas/yangli45/summary/ITL4GL2.w5 384 96 0.01 sum 1058 ATAC:ITL4GL2 +1059 yangli46 /home/drk/tillage/datasets/mouse/atac/catlas/yangli46/summary/ITL5GL1.w5 384 96 0.01 sum 1059 ATAC:ITL5GL1 +1060 yangli47 /home/drk/tillage/datasets/mouse/atac/catlas/yangli47/summary/ITL5GL2.w5 384 96 0.01 sum 1060 ATAC:ITL5GL2 +1061 yangli48 /home/drk/tillage/datasets/mouse/atac/catlas/yangli48/summary/ITL5GL3.w5 384 96 0.01 sum 1061 ATAC:ITL5GL3 +1062 yangli49 /home/drk/tillage/datasets/mouse/atac/catlas/yangli49/summary/ITL6GL1.w5 384 96 0.01 sum 1062 ATAC:ITL6GL1 +1063 yangli5 /home/drk/tillage/datasets/mouse/atac/catlas/yangli5/summary/CA1GL2.w5 384 96 0.01 sum 1063 ATAC:CA1GL2 +1064 yangli50 /home/drk/tillage/datasets/mouse/atac/catlas/yangli50/summary/ITL6GL2.w5 384 96 0.01 sum 1064 ATAC:ITL6GL2 +1065 yangli51 /home/drk/tillage/datasets/mouse/atac/catlas/yangli51/summary/ITL6GL3.w5 384 96 0.01 sum 1065 ATAC:ITL6GL3 +1066 yangli52 /home/drk/tillage/datasets/mouse/atac/catlas/yangli52/summary/ITL6GL4.w5 384 96 0.01 sum 1066 ATAC:ITL6GL4 +1067 yangli53 /home/drk/tillage/datasets/mouse/atac/catlas/yangli53/summary/ITL6GL5.w5 384 96 0.01 sum 1067 ATAC:ITL6GL5 +1068 yangli54 /home/drk/tillage/datasets/mouse/atac/catlas/yangli54/summary/ITL6GL6.w5 384 96 0.01 sum 1068 ATAC:ITL6GL6 +1069 yangli55 /home/drk/tillage/datasets/mouse/atac/catlas/yangli55/summary/L6bGL1.w5 384 96 0.01 sum 1069 ATAC:L6bGL1 +1070 yangli56 /home/drk/tillage/datasets/mouse/atac/catlas/yangli56/summary/L6bGL2.w5 384 96 0.01 sum 1070 ATAC:L6bGL2 +1071 yangli57 /home/drk/tillage/datasets/mouse/atac/catlas/yangli57/summary/L6bGL3.w5 384 96 0.01 sum 1071 ATAC:L6bGL3 +1072 yangli58 /home/drk/tillage/datasets/mouse/atac/catlas/yangli58/summary/L6bGL4.w5 384 96 0.01 sum 1072 ATAC:L6bGL4 +1073 yangli59 /home/drk/tillage/datasets/mouse/atac/catlas/yangli59/summary/L6bGL5.w5 384 96 0.01 sum 1073 ATAC:L6bGL5 +1074 yangli6 /home/drk/tillage/datasets/mouse/atac/catlas/yangli6/summary/CA1GL3.w5 384 96 0.01 sum 1074 ATAC:CA1GL3 +1075 yangli60 /home/drk/tillage/datasets/mouse/atac/catlas/yangli60/summary/L6bGL6.w5 384 96 0.01 sum 1075 ATAC:L6bGL6 +1076 yangli61 /home/drk/tillage/datasets/mouse/atac/catlas/yangli61/summary/LAMGA1.w5 384 96 0.01 sum 1076 ATAC:LAMGA1 +1077 yangli62 /home/drk/tillage/datasets/mouse/atac/catlas/yangli62/summary/LAMGA2.w5 384 96 0.01 sum 1077 ATAC:LAMGA2 +1078 yangli63 /home/drk/tillage/datasets/mouse/atac/catlas/yangli63/summary/LAMGA3.w5 384 96 0.01 sum 1078 ATAC:LAMGA3 +1079 yangli64 /home/drk/tillage/datasets/mouse/atac/catlas/yangli64/summary/LAMGA4.w5 384 96 0.01 sum 1079 ATAC:LAMGA4 +1080 yangli65 /home/drk/tillage/datasets/mouse/atac/catlas/yangli65/summary/LSXGA1.w5 384 96 0.01 sum 1080 ATAC:LSXGA1 +1081 yangli66 /home/drk/tillage/datasets/mouse/atac/catlas/yangli66/summary/LSXGA2.w5 384 96 0.01 sum 1081 ATAC:LSXGA2 +1082 yangli67 /home/drk/tillage/datasets/mouse/atac/catlas/yangli67/summary/LSXGA3.w5 384 96 0.01 sum 1082 ATAC:LSXGA3 +1083 yangli68 /home/drk/tillage/datasets/mouse/atac/catlas/yangli68/summary/LSXGA4.w5 384 96 0.01 sum 1083 ATAC:LSXGA4 +1084 yangli69 /home/drk/tillage/datasets/mouse/atac/catlas/yangli69/summary/LSXGA5.w5 384 96 0.01 sum 1084 ATAC:LSXGA5 +1085 yangli7 /home/drk/tillage/datasets/mouse/atac/catlas/yangli7/summary/CA3GL1.w5 384 96 0.01 sum 1085 ATAC:CA3GL1 +1086 yangli70 /home/drk/tillage/datasets/mouse/atac/catlas/yangli70/summary/LSXGA6.w5 384 96 0.01 sum 1086 ATAC:LSXGA6 +1087 yangli71 /home/drk/tillage/datasets/mouse/atac/catlas/yangli71/summary/LSXGA7.w5 384 96 0.01 sum 1087 ATAC:LSXGA7 +1088 yangli72 /home/drk/tillage/datasets/mouse/atac/catlas/yangli72/summary/MFOL.w5 384 96 0.01 sum 1088 ATAC:MFOL +1089 yangli73 /home/drk/tillage/datasets/mouse/atac/catlas/yangli73/summary/MGL.w5 384 96 0.01 sum 1089 ATAC:MGL +1090 yangli74 /home/drk/tillage/datasets/mouse/atac/catlas/yangli74/summary/MOL.w5 384 96 0.01 sum 1090 ATAC:MOL +1091 yangli75 /home/drk/tillage/datasets/mouse/atac/catlas/yangli75/summary/MSGA1.w5 384 96 0.01 sum 1091 ATAC:MSGA1 +1092 yangli76 /home/drk/tillage/datasets/mouse/atac/catlas/yangli76/summary/MSGA10.w5 384 96 0.01 sum 1092 ATAC:MSGA10 +1093 yangli77 /home/drk/tillage/datasets/mouse/atac/catlas/yangli77/summary/MSGA11.w5 384 96 0.01 sum 1093 ATAC:MSGA11 +1094 yangli78 /home/drk/tillage/datasets/mouse/atac/catlas/yangli78/summary/MSGA12.w5 384 96 0.01 sum 1094 ATAC:MSGA12 +1095 yangli79 /home/drk/tillage/datasets/mouse/atac/catlas/yangli79/summary/MSGA13.w5 384 96 0.01 sum 1095 ATAC:MSGA13 +1096 yangli8 /home/drk/tillage/datasets/mouse/atac/catlas/yangli8/summary/CA3GL2.w5 384 96 0.01 sum 1096 ATAC:CA3GL2 +1097 yangli80 /home/drk/tillage/datasets/mouse/atac/catlas/yangli80/summary/MSGA2.w5 384 96 0.01 sum 1097 ATAC:MSGA2 +1098 yangli81 /home/drk/tillage/datasets/mouse/atac/catlas/yangli81/summary/MSGA3.w5 384 96 0.01 sum 1098 ATAC:MSGA3 +1099 yangli82 /home/drk/tillage/datasets/mouse/atac/catlas/yangli82/summary/MSGA4.w5 384 96 0.01 sum 1099 ATAC:MSGA4 +1100 yangli83 /home/drk/tillage/datasets/mouse/atac/catlas/yangli83/summary/MSGA5.w5 384 96 0.01 sum 1100 ATAC:MSGA5 +1101 yangli84 /home/drk/tillage/datasets/mouse/atac/catlas/yangli84/summary/MSGA6.w5 384 96 0.01 sum 1101 ATAC:MSGA6 +1102 yangli85 /home/drk/tillage/datasets/mouse/atac/catlas/yangli85/summary/MSGA7.w5 384 96 0.01 sum 1102 ATAC:MSGA7 +1103 yangli86 /home/drk/tillage/datasets/mouse/atac/catlas/yangli86/summary/MSGA8.w5 384 96 0.01 sum 1103 ATAC:MSGA8 +1104 yangli87 /home/drk/tillage/datasets/mouse/atac/catlas/yangli87/summary/MSGA9.w5 384 96 0.01 sum 1104 ATAC:MSGA9 +1105 yangli88 /home/drk/tillage/datasets/mouse/atac/catlas/yangli88/summary/MXD.w5 384 96 0.01 sum 1105 ATAC:MXD +1106 yangli89 /home/drk/tillage/datasets/mouse/atac/catlas/yangli89/summary/NFOL.w5 384 96 0.01 sum 1106 ATAC:NFOL +1107 yangli9 /home/drk/tillage/datasets/mouse/atac/catlas/yangli9/summary/CA3GL3.w5 384 96 0.01 sum 1107 ATAC:CA3GL3 +1108 yangli90 /home/drk/tillage/datasets/mouse/atac/catlas/yangli90/summary/NIPC.w5 384 96 0.01 sum 1108 ATAC:NIPC +1109 yangli91 /home/drk/tillage/datasets/mouse/atac/catlas/yangli91/summary/NPGL1.w5 384 96 0.01 sum 1109 ATAC:NPGL1 +1110 yangli92 /home/drk/tillage/datasets/mouse/atac/catlas/yangli92/summary/NPGL2.w5 384 96 0.01 sum 1110 ATAC:NPGL2 +1111 yangli93 /home/drk/tillage/datasets/mouse/atac/catlas/yangli93/summary/NPGL3.w5 384 96 0.01 sum 1111 ATAC:NPGL3 +1112 yangli94 /home/drk/tillage/datasets/mouse/atac/catlas/yangli94/summary/NPGL4.w5 384 96 0.01 sum 1112 ATAC:NPGL4 +1113 yangli95 /home/drk/tillage/datasets/mouse/atac/catlas/yangli95/summary/NPGL5.w5 384 96 0.01 sum 1113 ATAC:NPGL5 +1114 yangli96 /home/drk/tillage/datasets/mouse/atac/catlas/yangli96/summary/OBDOP1.w5 384 96 0.01 sum 1114 ATAC:OBDOP1 +1115 yangli97 /home/drk/tillage/datasets/mouse/atac/catlas/yangli97/summary/OBDOP2.w5 384 96 0.01 sum 1115 ATAC:OBDOP2 +1116 yangli98 /home/drk/tillage/datasets/mouse/atac/catlas/yangli98/summary/OBGA1.w5 384 96 0.01 sum 1116 ATAC:OBGA1 +1117 yangli99 /home/drk/tillage/datasets/mouse/atac/catlas/yangli99/summary/OBGA2.w5 384 96 0.01 sum 1117 ATAC:OBGA2 +1118 ENCFF426ODS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADI/summary/ENCFF426ODS.w5 128 32 2.0 mean 1118 CHIP:H3K4me3:B10.H-2aH-4bp/Wts CH12.LX +1119 ENCFF993SYN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADK/summary/ENCFF993SYN.w5 128 32 2.0 mean 1119 CHIP:H3K4me1:129 ES-E14 +1120 ENCFF240MDV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADL/summary/ENCFF240MDV.w5 128 32 2.0 mean 1120 CHIP:H3K4me3:129 ES-E14 +1121 ENCFF325GQU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADM/summary/ENCFF325GQU.w5 128 32 2.0 mean 1121 CHIP:H3K9me3:129 ES-E14 +1122 ENCFF409ARU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADP/summary/ENCFF409ARU.w5 128 32 2.0 mean 1122 CHIP:H3K27me3:DBA/2 MEL cell line +1123 ENCFF070ZCF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADQ/summary/ENCFF070ZCF.w5 128 32 2.0 mean 1123 CHIP:H3K4me1:DBA/2 MEL cell line +1124 ENCFF583MBD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADR/summary/ENCFF583MBD.w5 128 32 2.0 mean 1124 CHIP:H3K4me3:DBA/2 MEL cell line +1125 ENCFF089WYW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADT/summary/ENCFF089WYW.w5 128 32 2.0 mean 1125 CHIP:H3K9me3:DBA/2 MEL cell line +1126 ENCFF268EAZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADW/summary/ENCFF268EAZ.w5 128 32 2.0 mean 1126 CHIP:H3K27me3:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1127 ENCFF981EVL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADX/summary/ENCFF981EVL.w5 128 32 2.0 mean 1127 CHIP:H3K36me3:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1128 ENCFF335VHL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ADY/summary/ENCFF335VHL.w5 128 32 2.0 mean 1128 CHIP:H3K4me1:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1129 ENCFF206DMH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AEA/summary/ENCFF206DMH.w5 128 32 2.0 mean 1129 CHIP:H3K4me3:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1130 ENCFF393FAV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AEB/summary/ENCFF393FAV.w5 128 32 2.0 mean 1130 CHIP:H3K9me3:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1131 ENCFF517JPC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHL/summary/ENCFF517JPC.w5 128 32 2.0 mean 1131 CHIP:H3K36me3:C3H C2C12 +1132 ENCFF488BZX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHM/summary/ENCFF488BZX.w5 128 32 2.0 mean 1132 CHIP:H3K27me3:C3H myocyte originated from C2C12 +1133 ENCFF388RKS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHN/summary/ENCFF388RKS.w5 128 32 2.0 mean 1133 CHIP:H3K79me2:C3H myocyte originated from C2C12 +1134 ENCFF436ZSV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHO/summary/ENCFF436ZSV.w5 128 32 2.0 mean 1134 CHIP:H3K4me3:C3H C2C12 +1135 ENCFF696NHF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHP/summary/ENCFF696NHF.w5 128 32 2.0 mean 1135 CHIP:H3ac:C3H C2C12 +1136 ENCFF442ENM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHQ/summary/ENCFF442ENM.w5 128 32 2.0 mean 1136 CHIP:H3K79me2:C3H C2C12 +1137 ENCFF962JNF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHR/summary/ENCFF962JNF.w5 128 32 2.0 mean 1137 CHIP:H3K27me3:C3H C2C12 +1138 ENCFF245DME /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHS/summary/ENCFF245DME.w5 128 32 2.0 mean 1138 CHIP:H3K4me2:C3H myocyte originated from C2C12 +1139 ENCFF518CXM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHT/summary/ENCFF518CXM.w5 128 32 2.0 mean 1139 CHIP:H3K4me3:C3H myocyte originated from C2C12 +1140 ENCFF222EBN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHU/summary/ENCFF222EBN.w5 128 32 2.0 mean 1140 CHIP:H3ac:C3H myocyte originated from C2C12 +1141 ENCFF046UQY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHV/summary/ENCFF046UQY.w5 128 32 2.0 mean 1141 CHIP:H3K36me3:C3H myocyte originated from C2C12 +1142 ENCFF921JTJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AHW/summary/ENCFF921JTJ.w5 128 32 2.0 mean 1142 CHIP:H3K79me3:C3H C2C12 +1143 ENCFF096FAR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIB/summary/ENCFF096FAR.w5 128 32 2.0 mean 1143 CHIP:CEBPB:C3H myocyte originated from C2C12 +1144 ENCFF059BXG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIC/summary/ENCFF059BXG.w5 128 32 2.0 mean 1144 CHIP:MYOG:C3H myocyte originated from C2C12 +1145 ENCFF891VZV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AID/summary/ENCFF891VZV.w5 128 32 2.0 mean 1145 CHIP:MYOG:C3H myocyte originated from C2C12 +1146 ENCFF170WKG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIE/summary/ENCFF170WKG.w5 128 32 2.0 mean 1146 CHIP:USF1:C3H myocyte originated from C2C12 +1147 ENCFF462ONT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIG/summary/ENCFF462ONT.w5 128 32 2.0 mean 1147 CHIP:MYOD1:C3H C2C12 +1148 ENCFF779WLW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIH/summary/ENCFF779WLW.w5 128 32 2.0 mean 1148 CHIP:MYOD1:C3H myocyte originated from C2C12 +1149 ENCFF528UTW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AII/summary/ENCFF528UTW.w5 128 32 2.0 mean 1149 CHIP:E2F4:C3H myocyte originated from C2C12 +1150 ENCFF583QSM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIJ/summary/ENCFF583QSM.w5 128 32 2.0 mean 1150 CHIP:CTCF:C3H C2C12 +1151 ENCFF595PRV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIL/summary/ENCFF595PRV.w5 128 32 2.0 mean 1151 CHIP:MAX:C3H myocyte originated from C2C12 +1152 ENCFF552PFK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIM/summary/ENCFF552PFK.w5 128 32 2.0 mean 1152 CHIP:SRF:C3H myocyte originated from C2C12 +1153 ENCFF247PFV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIN/summary/ENCFF247PFV.w5 128 32 2.0 mean 1153 CHIP:TCF12:C3H myocyte originated from C2C12 +1154 ENCFF862HLX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIO/summary/ENCFF862HLX.w5 128 32 2.0 mean 1154 CHIP:MAX:C3H C2C12 +1155 ENCFF565MVR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIP/summary/ENCFF565MVR.w5 128 32 2.0 mean 1155 CHIP:TCF3:C3H myocyte originated from C2C12 +1156 ENCFF602DCT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIQ/summary/ENCFF602DCT.w5 128 32 2.0 mean 1156 CHIP:USF1:C3H C2C12 +1157 ENCFF539PGU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIR/summary/ENCFF539PGU.w5 128 32 2.0 mean 1157 CHIP:MYOD1:C3H myocyte originated from C2C12 +1158 ENCFF967HVW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIS/summary/ENCFF967HVW.w5 128 32 2.0 mean 1158 CHIP:REST:C3H myocyte originated from C2C12 +1159 ENCFF122ZAR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIT/summary/ENCFF122ZAR.w5 128 32 2.0 mean 1159 CHIP:MYOD1:C3H myocyte originated from C2C12 +1160 ENCFF323UQU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIU/summary/ENCFF323UQU.w5 128 32 2.0 mean 1160 CHIP:POLR2AphosphoS2:C3H myocyte originated from C2C12 +1161 ENCFF674URL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIV/summary/ENCFF674URL.w5 128 32 2.0 mean 1161 CHIP:CEBPB:C3H C2C12 +1162 ENCFF140UCV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIW/summary/ENCFF140UCV.w5 128 32 2.0 mean 1162 CHIP:MYOG:C3H myocyte originated from C2C12 +1163 ENCFF680DPI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000AIX/summary/ENCFF680DPI.w5 128 32 2.0 mean 1163 CHIP:POLR2A:C3H myocyte originated from C2C12 +1164 ENCFF021EDM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAE/summary/ENCFF021EDM.w5 128 32 2.0 mean 1164 CHIP:H3K4me1:C57BL/6 heart male adult (8 weeks) +1165 ENCFF192PPW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAF/summary/ENCFF192PPW.w5 128 32 2.0 mean 1165 CHIP:H3K4me1:C57BL/6 kidney male adult (8 weeks) +1166 ENCFF518BJU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAG/summary/ENCFF518BJU.w5 128 32 2.0 mean 1166 CHIP:H3K4me1:C57BL/6 bone marrow male adult (8 weeks) +1167 ENCFF620KTZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAH/summary/ENCFF620KTZ.w5 128 32 2.0 mean 1167 CHIP:H3K4me3:C57BL/6 bone marrow male adult (8 weeks) +1168 ENCFF815CFZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAI/summary/ENCFF815CFZ.w5 128 32 2.0 mean 1168 CHIP:H3K4me1:C57BL/6 cortical plate male adult (8 weeks) +1169 ENCFF288SAJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAK/summary/ENCFF288SAJ.w5 128 32 2.0 mean 1169 CHIP:H3K4me3:C57BL/6 cerebellum male adult (8 weeks) +1170 ENCFF827AKI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAL/summary/ENCFF827AKI.w5 128 32 2.0 mean 1170 CHIP:H3K4me1:C57BL/6 cerebellum male adult (8 weeks) +1171 ENCFF118SXS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAM/summary/ENCFF118SXS.w5 128 32 2.0 mean 1171 CHIP:H3K4me3:C57BL/6 heart male adult (8 weeks) +1172 ENCFF177YGH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAN/summary/ENCFF177YGH.w5 128 32 2.0 mean 1172 CHIP:H3K4me3:C57BL/6 kidney male adult (8 weeks) +1173 ENCFF881VZQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAO/summary/ENCFF881VZQ.w5 128 32 2.0 mean 1173 CHIP:H3K4me1:C57BL/6 liver male adult (8 weeks) +1174 ENCFF753IXB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAP/summary/ENCFF753IXB.w5 128 32 2.0 mean 1174 CHIP:H3K4me3:C57BL/6 liver male adult (8 weeks) +1175 ENCFF206LES /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAQ/summary/ENCFF206LES.w5 128 32 2.0 mean 1175 CHIP:H3K4me1:C57BL/6 lung male adult (8 weeks) +1176 ENCFF353PNU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CAZ/summary/ENCFF353PNU.w5 128 32 2.0 mean 1176 CHIP:H3K4me1:C57BL/6 embryonic fibroblast male embryo (13.5 weeks) +1177 ENCFF379VFT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBA/summary/ENCFF379VFT.w5 128 32 2.0 mean 1177 CHIP:H3K4me3:C57BL/6 embryonic fibroblast male embryo (13.5 weeks) +1178 ENCFF202RFR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBC/summary/ENCFF202RFR.w5 128 32 2.0 mean 1178 CHIP:H3K4me1:C57BL/6 spleen male adult (8 weeks) +1179 ENCFF295HDA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBF/summary/ENCFF295HDA.w5 128 32 2.0 mean 1179 CHIP:H3K4me1:C57BL/6 ES-Bruce4 +1180 ENCFF363JJV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBG/summary/ENCFF363JJV.w5 128 32 2.0 mean 1180 CHIP:H3K4me3:C57BL/6 ES-Bruce4 +1181 ENCFF639AFA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBI/summary/ENCFF639AFA.w5 128 32 2.0 mean 1181 CHIP:CTCF:C57BL/6 heart male adult (8 weeks) +1182 ENCFF164ZFD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBJ/summary/ENCFF164ZFD.w5 128 32 2.0 mean 1182 CHIP:CTCF:C57BL/6 kidney male adult (8 weeks) +1183 ENCFF916PLK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBK/summary/ENCFF916PLK.w5 128 32 2.0 mean 1183 CHIP:POLR2A:C57BL/6 kidney male adult (8 weeks) +1184 ENCFF156BYW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBL/summary/ENCFF156BYW.w5 128 32 2.0 mean 1184 CHIP:CTCF:C57BL/6 bone marrow male adult (8 weeks) +1185 ENCFF595EFE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBM/summary/ENCFF595EFE.w5 128 32 2.0 mean 1185 CHIP:POLR2A:C57BL/6 bone marrow male adult (8 weeks) +1186 ENCFF867MOQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBN/summary/ENCFF867MOQ.w5 128 32 2.0 mean 1186 CHIP:CTCF:C57BL/6 cerebellum male adult (8 weeks) +1187 ENCFF625PME /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBQ/summary/ENCFF625PME.w5 128 32 2.0 mean 1187 CHIP:POLR2A:C57BL/6 cerebellum male adult (8 weeks) +1188 ENCFF868AOT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBS/summary/ENCFF868AOT.w5 128 32 2.0 mean 1188 CHIP:POLR2A:C57BL/6 heart male adult (8 weeks) +1189 ENCFF919KIP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBU/summary/ENCFF919KIP.w5 128 32 2.0 mean 1189 CHIP:CTCF:C57BL/6 liver male adult (8 weeks) +1190 ENCFF538KBR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBV/summary/ENCFF538KBR.w5 128 32 2.0 mean 1190 CHIP:CTCF:C57BL/6 lung male adult (8 weeks) +1191 ENCFF432JCZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBW/summary/ENCFF432JCZ.w5 128 32 2.0 mean 1191 CHIP:CTCF:C57BL/6 embryonic fibroblast male embryo (13.5 weeks) +1192 ENCFF378CWR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBX/summary/ENCFF378CWR.w5 128 32 2.0 mean 1192 CHIP:POLR2A:C57BL/6 embryonic fibroblast male embryo (13.5 weeks) +1193 ENCFF376VCU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CBZ/summary/ENCFF376VCU.w5 128 32 2.0 mean 1193 CHIP:POLR2A:C57BL/6 spleen male adult (8 weeks) +1194 ENCFF852EDW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCA/summary/ENCFF852EDW.w5 128 32 2.0 mean 1194 CHIP:EP300:C57BL/6 heart male adult (8 weeks) +1195 ENCFF339GSH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCB/summary/ENCFF339GSH.w5 128 32 2.0 mean 1195 CHIP:CTCF:C57BL/6 ES-Bruce4 +1196 ENCFF040HIS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCC/summary/ENCFF040HIS.w5 128 32 2.0 mean 1196 CHIP:POLR2A:C57BL/6 ES-Bruce4 +1197 ENCFF320LZI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCD/summary/ENCFF320LZI.w5 128 32 2.0 mean 1197 CHIP:EP300:C57BL/6 ES-Bruce4 +1198 ENCFF669DNL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCE/summary/ENCFF669DNL.w5 128 32 2.0 mean 1198 CHIP:H3K27ac:C57BL/6 olfactory bulb male adult (8 weeks) +1199 ENCFF733KTU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCF/summary/ENCFF733KTU.w5 128 32 2.0 mean 1199 CHIP:H3K4me1:C57BL/6 olfactory bulb male adult (8 weeks) +1200 ENCFF354DWX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCH/summary/ENCFF354DWX.w5 128 32 2.0 mean 1200 CHIP:H3K27ac:C57BL/6 thymus male adult (8 weeks) +1201 ENCFF666XCJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCI/summary/ENCFF666XCJ.w5 128 32 2.0 mean 1201 CHIP:H3K4me1:C57BL/6 thymus male adult (8 weeks) +1202 ENCFF810PIW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCJ/summary/ENCFF810PIW.w5 128 32 2.0 mean 1202 CHIP:H3K4me3:C57BL/6 thymus male adult (8 weeks) +1203 ENCFF692OFZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCL/summary/ENCFF692OFZ.w5 128 32 2.0 mean 1203 CHIP:H3K27ac:C57BL/6 bone marrow male adult (8 weeks) +1204 ENCFF212SMS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCQ/summary/ENCFF212SMS.w5 128 32 2.0 mean 1204 CHIP:H3K27ac:C57BL/6 small intestine male adult (8 weeks) +1205 ENCFF159RUF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCR/summary/ENCFF159RUF.w5 128 32 2.0 mean 1205 CHIP:H3K4me1:C57BL/6 small intestine male adult (8 weeks) +1206 ENCFF032JSS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCS/summary/ENCFF032JSS.w5 128 32 2.0 mean 1206 CHIP:H3K4me3:C57BL/6 small intestine male adult (8 weeks) +1207 ENCFF572JFH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCU/summary/ENCFF572JFH.w5 128 32 2.0 mean 1207 CHIP:H3K27ac:C57BL/6 testis male adult (8 weeks) +1208 ENCFF073HRX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCV/summary/ENCFF073HRX.w5 128 32 2.0 mean 1208 CHIP:H3K4me1:C57BL/6 testis male adult (8 weeks) +1209 ENCFF147BMC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CCW/summary/ENCFF147BMC.w5 128 32 2.0 mean 1209 CHIP:H3K4me3:C57BL/6 testis male adult (8 weeks) +1210 ENCFF234IJR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDC/summary/ENCFF234IJR.w5 128 32 2.0 mean 1210 CHIP:H3K27ac:C57BL/6 cerebellum male adult (8 weeks) +1211 ENCFF619CVT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDD/summary/ENCFF619CVT.w5 128 32 2.0 mean 1211 CHIP:H3K27ac:C57BL/6 cortical plate male adult (8 weeks) +1212 ENCFF124CBV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDE/summary/ENCFF124CBV.w5 128 32 2.0 mean 1212 CHIP:H3K27ac:C57BL/6 ES-Bruce4 +1213 ENCFF691YDA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDF/summary/ENCFF691YDA.w5 128 32 2.0 mean 1213 CHIP:H3K27ac:C57BL/6 heart male adult (8 weeks) +1214 ENCFF188DKO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDG/summary/ENCFF188DKO.w5 128 32 2.0 mean 1214 CHIP:H3K27ac:C57BL/6 kidney male adult (8 weeks) +1215 ENCFF632VNQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDH/summary/ENCFF632VNQ.w5 128 32 2.0 mean 1215 CHIP:H3K27ac:C57BL/6 liver male adult (8 weeks) +1216 ENCFF387JGJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDI/summary/ENCFF387JGJ.w5 128 32 2.0 mean 1216 CHIP:H3K27ac:C57BL/6 embryonic fibroblast male embryo (13.5 weeks) +1217 ENCFF470WIY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDJ/summary/ENCFF470WIY.w5 128 32 2.0 mean 1217 CHIP:H3K27ac:C57BL/6 spleen male adult (8 weeks) +1218 ENCFF034YQZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDK/summary/ENCFF034YQZ.w5 128 32 2.0 mean 1218 CHIP:H3K27ac:C57BL/6 heart embryo (14.5 days) +1219 ENCFF415BLI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDL/summary/ENCFF415BLI.w5 128 32 2.0 mean 1219 CHIP:H3K4me1:C57BL/6 heart embryo (14.5 days) +1220 ENCFF227BHG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDM/summary/ENCFF227BHG.w5 128 32 2.0 mean 1220 CHIP:H3K4me3:C57BL/6 heart embryo (14.5 days) +1221 ENCFF924IWW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDO/summary/ENCFF924IWW.w5 128 32 2.0 mean 1221 CHIP:H3K27ac:C57BL/6 placenta female adult (8 weeks) +1222 ENCFF844ZFQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDP/summary/ENCFF844ZFQ.w5 128 32 2.0 mean 1222 CHIP:H3K4me1:C57BL/6 placenta female adult (8 weeks) +1223 ENCFF235ZAJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDQ/summary/ENCFF235ZAJ.w5 128 32 2.0 mean 1223 CHIP:H3K4me3:C57BL/6 placenta female adult (8 weeks) +1224 ENCFF069XTE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDS/summary/ENCFF069XTE.w5 128 32 2.0 mean 1224 CHIP:H3K4me3:C57BL/6 olfactory bulb male adult (8 weeks) +1225 ENCFF506KCT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDU/summary/ENCFF506KCT.w5 128 32 2.0 mean 1225 CHIP:H3K27ac:C57BL/6 liver embryo (14.5 days) +1226 ENCFF309BER /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDV/summary/ENCFF309BER.w5 128 32 2.0 mean 1226 CHIP:H3K4me3:C57BL/6 liver embryo (14.5 days) +1227 ENCFF850QFU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDW/summary/ENCFF850QFU.w5 128 32 2.0 mean 1227 CHIP:H3K4me1:C57BL/6 liver embryo (14.5 days) +1228 ENCFF193PLE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CDY/summary/ENCFF193PLE.w5 128 32 2.0 mean 1228 CHIP:POLR2A:C57BL/6 olfactory bulb male adult (8 weeks) +1229 ENCFF820TWT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEE/summary/ENCFF820TWT.w5 128 32 2.0 mean 1229 CHIP:POLR2A:C57BL/6 small intestine male adult (8 weeks) +1230 ENCFF946MNK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEF/summary/ENCFF946MNK.w5 128 32 2.0 mean 1230 CHIP:CTCF:C57BL/6 testis male adult (8 weeks) +1231 ENCFF333YCZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEG/summary/ENCFF333YCZ.w5 128 32 2.0 mean 1231 CHIP:POLR2A:C57BL/6 testis male adult (8 weeks) +1232 ENCFF344SFV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEJ/summary/ENCFF344SFV.w5 128 32 2.0 mean 1232 CHIP:H3K27me3:C57BL/6 heart male adult (8 weeks) +1233 ENCFF865YFU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEK/summary/ENCFF865YFU.w5 128 32 2.0 mean 1233 CHIP:H3K36me3:C57BL/6 heart male adult (8 weeks) +1234 ENCFF042INO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEL/summary/ENCFF042INO.w5 128 32 2.0 mean 1234 CHIP:H3K79me2:C57BL/6 heart male adult (8 weeks) +1235 ENCFF421ODL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEM/summary/ENCFF421ODL.w5 128 32 2.0 mean 1235 CHIP:H3K9ac:C57BL/6 heart male adult (8 weeks) +1236 ENCFF172GJQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEN/summary/ENCFF172GJQ.w5 128 32 2.0 mean 1236 CHIP:H3K27me3:C57BL/6 liver male adult (8 weeks) +1237 ENCFF093JJJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEO/summary/ENCFF093JJJ.w5 128 32 2.0 mean 1237 CHIP:H3K36me3:C57BL/6 liver male adult (8 weeks) +1238 ENCFF157PQZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEP/summary/ENCFF157PQZ.w5 128 32 2.0 mean 1238 CHIP:H3K79me2:C57BL/6 liver male adult (8 weeks) +1239 ENCFF265TCP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEQ/summary/ENCFF265TCP.w5 128 32 2.0 mean 1239 CHIP:H3K9ac:C57BL/6 liver male adult (8 weeks) +1240 ENCFF029TZQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CER/summary/ENCFF029TZQ.w5 128 32 2.0 mean 1240 CHIP:H3K27me3:DBA/2 MEL cell line +1241 ENCFF207HCQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CES/summary/ENCFF207HCQ.w5 128 32 2.0 mean 1241 CHIP:H3K36me3:DBA/2 MEL cell line +1242 ENCFF279GJP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CET/summary/ENCFF279GJP.w5 128 32 2.0 mean 1242 CHIP:H3K79me2:DBA/2 MEL cell line +1243 ENCFF603CPU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEU/summary/ENCFF603CPU.w5 128 32 2.0 mean 1243 CHIP:H3K9ac:DBA/2 MEL cell line +1244 ENCFF414TDD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEV/summary/ENCFF414TDD.w5 128 32 2.0 mean 1244 CHIP:H3K27ac:DBA/2 MEL cell line +1245 ENCFF488XKH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEW/summary/ENCFF488XKH.w5 128 32 2.0 mean 1245 CHIP:H3K4me1:DBA/2 MEL cell line +1246 ENCFF496UKK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEX/summary/ENCFF496UKK.w5 128 32 2.0 mean 1246 CHIP:H3K4me3:DBA/2 MEL cell line +1247 ENCFF012PBY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CEZ/summary/ENCFF012PBY.w5 128 32 2.0 mean 1247 CHIP:H3K27ac:C57BL/6 brown adipose tissue male adult (24 weeks) +1248 ENCFF494KRZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFA/summary/ENCFF494KRZ.w5 128 32 2.0 mean 1248 CHIP:H3K4me1:C57BL/6 brown adipose tissue male adult (24 weeks) +1249 ENCFF966UOI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFB/summary/ENCFF966UOI.w5 128 32 2.0 mean 1249 CHIP:H3K4me3:C57BL/6 brown adipose tissue male adult (24 weeks) +1250 ENCFF668SMR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFD/summary/ENCFF668SMR.w5 128 32 2.0 mean 1250 CHIP:H3K27ac:C57BL/6 bone marrow macrophage male adult (8 weeks) +1251 ENCFF167PJA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFE/summary/ENCFF167PJA.w5 128 32 2.0 mean 1251 CHIP:H3K4me1:C57BL/6 bone marrow macrophage male adult (8 weeks) +1252 ENCFF186XGM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFF/summary/ENCFF186XGM.w5 128 32 2.0 mean 1252 CHIP:H3K4me3:C57BL/6 bone marrow macrophage male adult (8 weeks) +1253 ENCFF771PZS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFH/summary/ENCFF771PZS.w5 128 32 2.0 mean 1253 CHIP:CTCF:DBA/2 MEL cell line +1254 ENCFF218UAZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFI/summary/ENCFF218UAZ.w5 128 32 2.0 mean 1254 CHIP:POLR2A:DBA/2 MEL cell line +1255 ENCFF826OQW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFJ/summary/ENCFF826OQW.w5 128 32 2.0 mean 1255 CHIP:CTCF:C57BL/6 bone marrow macrophage male adult (8 weeks) +1256 ENCFF575UNY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFK/summary/ENCFF575UNY.w5 128 32 2.0 mean 1256 CHIP:POLR2A:C57BL/6 bone marrow macrophage male adult (8 weeks) +1257 ENCFF863PEU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFL/summary/ENCFF863PEU.w5 128 32 2.0 mean 1257 CHIP:H3K36me3:B10.H-2aH-4bp/Wts CH12.LX +1258 ENCFF614WMD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFM/summary/ENCFF614WMD.w5 128 32 2.0 mean 1258 CHIP:H3K27me3:C57BL/6 cerebellum male adult (8 weeks) +1259 ENCFF316WWL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFN/summary/ENCFF316WWL.w5 128 32 2.0 mean 1259 CHIP:H3K27me3:C57BL/6 ES-Bruce4 +1260 ENCFF109YST /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFO/summary/ENCFF109YST.w5 128 32 2.0 mean 1260 CHIP:H3K36me3:C57BL/6 ES-Bruce4 +1261 ENCFF324KCF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFP/summary/ENCFF324KCF.w5 128 32 2.0 mean 1261 CHIP:H3K27me3:C57BL/6 kidney male adult (8 weeks) +1262 ENCFF175AIB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFQ/summary/ENCFF175AIB.w5 128 32 2.0 mean 1262 CHIP:H3K36me3:C57BL/6 kidney male adult (8 weeks) +1263 ENCFF906CRU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFR/summary/ENCFF906CRU.w5 128 32 2.0 mean 1263 CHIP:H3K27me3:C57BL/6 small intestine male adult (8 weeks) +1264 ENCFF204STH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFS/summary/ENCFF204STH.w5 128 32 2.0 mean 1264 CHIP:H3K36me3:C57BL/6 small intestine male adult (8 weeks) +1265 ENCFF911TSZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFT/summary/ENCFF911TSZ.w5 128 32 2.0 mean 1265 CHIP:H3K36me3:C57BL/6 spleen male adult (8 weeks) +1266 ENCFF974RAM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFU/summary/ENCFF974RAM.w5 128 32 2.0 mean 1266 CHIP:H3K36me3:C57BL/6 testis male adult (8 weeks) +1267 ENCFF287DIJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFV/summary/ENCFF287DIJ.w5 128 32 2.0 mean 1267 CHIP:H3K36me3:C57BL/6 thymus male adult (8 weeks) +1268 ENCFF655NSX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFX/summary/ENCFF655NSX.w5 128 32 2.0 mean 1268 CHIP:H3K27me3:C57BL/6 splenic B cell male adult (8 weeks) +1269 ENCFF198YXO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFY/summary/ENCFF198YXO.w5 128 32 2.0 mean 1269 CHIP:H3K36me3:C57BL/6 splenic B cell male adult (8 weeks) +1270 ENCFF857TIJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CFZ/summary/ENCFF857TIJ.w5 128 32 2.0 mean 1270 CHIP:H3K9me3:C57BL/6 ES-Bruce4 +1271 ENCFF576XZZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGA/summary/ENCFF576XZZ.w5 128 32 2.0 mean 1271 CHIP:H3K27me3:C57BL/6 spleen male adult (8 weeks) +1272 ENCFF443EON /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGB/summary/ENCFF443EON.w5 128 32 2.0 mean 1272 CHIP:H3K27me3:C57BL/6 testis male adult (8 weeks) +1273 ENCFF476YTS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGC/summary/ENCFF476YTS.w5 128 32 2.0 mean 1273 CHIP:H3K27me3:C57BL/6 thymus male adult (8 weeks) +1274 ENCFF819RQI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGH/summary/ENCFF819RQI.w5 128 32 2.0 mean 1274 CHIP:H3K4me1:B10.H-2aH-4bp/Wts CH12.LX +1275 ENCFF122GDX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGI/summary/ENCFF122GDX.w5 128 32 2.0 mean 1275 CHIP:H3K4me2:B10.H-2aH-4bp/Wts CH12.LX +1276 ENCFF867PYD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGJ/summary/ENCFF867PYD.w5 128 32 2.0 mean 1276 CHIP:H3K27ac:B10.H-2aH-4bp/Wts CH12.LX +1277 ENCFF500BXF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGK/summary/ENCFF500BXF.w5 128 32 2.0 mean 1277 CHIP:H3K4me3:B10.H-2aH-4bp/Wts CH12.LX +1278 ENCFF250LUT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGL/summary/ENCFF250LUT.w5 128 32 2.0 mean 1278 CHIP:H3K9ac:B10.H-2aH-4bp/Wts CH12.LX +1279 ENCFF840JAO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGM/summary/ENCFF840JAO.w5 128 32 2.0 mean 1279 CHIP:H3K79me2:B10.H-2aH-4bp/Wts CH12.LX +1280 ENCFF899GLT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGN/summary/ENCFF899GLT.w5 128 32 2.0 mean 1280 CHIP:H3K4me1:129 ES-E14 +1281 ENCFF857GJE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGO/summary/ENCFF857GJE.w5 128 32 2.0 mean 1281 CHIP:H3K4me3:129 ES-E14 +1282 ENCFF809IES /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGP/summary/ENCFF809IES.w5 128 32 2.0 mean 1282 CHIP:H3K9ac:129 ES-E14 +1283 ENCFF163HEV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGQ/summary/ENCFF163HEV.w5 128 32 2.0 mean 1283 CHIP:H3K27ac:129 ES-E14 +1284 ENCFF111CIF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGR/summary/ENCFF111CIF.w5 128 32 2.0 mean 1284 CHIP:H3K36me3:129 ES-E14 +1285 ENCFF609ZSZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000CGS/summary/ENCFF609ZSZ.w5 128 32 2.0 mean 1285 CHIP:H3K9ac:C57BL/6 ES-Bruce4 +1286 ENCFF460EAQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHD/summary/ENCFF460EAQ.w5 128 32 2.0 mean 1286 CHIP:FLI1:CD-1 megakaryocyte embryo (14.5 days) +1287 ENCFF331NCU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHF/summary/ENCFF331NCU.w5 128 32 2.0 mean 1287 CHIP:H3K27me3:CD-1 megakaryocyte embryo (14.5 days) +1288 ENCFF612WPA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHG/summary/ENCFF612WPA.w5 128 32 2.0 mean 1288 CHIP:H3K4me3:CD-1 erythroblast embryo (14.5 days) +1289 ENCFF851DGO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHH/summary/ENCFF851DGO.w5 128 32 2.0 mean 1289 CHIP:H3K9me3:CD-1 megakaryocyte embryo (14.5 days) +1290 ENCFF410HES /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHI/summary/ENCFF410HES.w5 128 32 2.0 mean 1290 CHIP:H3K36me3:CD-1 megakaryocyte embryo (14.5 days) +1291 ENCFF797MYD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHJ/summary/ENCFF797MYD.w5 128 32 2.0 mean 1291 CHIP:H3K9me3:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1292 ENCFF007WLT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHK/summary/ENCFF007WLT.w5 128 32 2.0 mean 1292 CHIP:H3K4me1:CD-1 erythroblast embryo (14.5 days) +1293 ENCFF034FFR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHL/summary/ENCFF034FFR.w5 128 32 2.0 mean 1293 CHIP:H3K36me3:CD-1 erythroblast embryo (14.5 days) +1294 ENCFF140MAG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHM/summary/ENCFF140MAG.w5 128 32 2.0 mean 1294 CHIP:H3K9me3:129 G1E +1295 ENCFF277AAJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHN/summary/ENCFF277AAJ.w5 128 32 2.0 mean 1295 CHIP:H3K9me3:CD-1 erythroblast embryo (14.5 days) +1296 ENCFF662VCX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHO/summary/ENCFF662VCX.w5 128 32 2.0 mean 1296 CHIP:H3K9me3:B10.H-2aH-4bp/Wts CH12.LX +1297 ENCFF220KWG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHP/summary/ENCFF220KWG.w5 128 32 2.0 mean 1297 CHIP:H3K27me3:CD-1 erythroblast embryo (14.5 days) +1298 ENCFF751XSP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHQ/summary/ENCFF751XSP.w5 128 32 2.0 mean 1298 CHIP:H3K4me1:B10.H-2aH-4bp/Wts CH12.LX +1299 ENCFF817HHK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHR/summary/ENCFF817HHK.w5 128 32 2.0 mean 1299 CHIP:H3K4me1:CD-1 megakaryocyte embryo (14.5 days) +1300 ENCFF750FWM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHS/summary/ENCFF750FWM.w5 128 32 2.0 mean 1300 CHIP:H3K36me3:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1301 ENCFF211IXB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHT/summary/ENCFF211IXB.w5 128 32 2.0 mean 1301 CHIP:H3K4me3:CD-1 megakaryocyte embryo (14.5 days) +1302 ENCFF288OKN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHU/summary/ENCFF288OKN.w5 128 32 2.0 mean 1302 CHIP:H3K4me3:B10.H-2aH-4bp/Wts CH12.LX +1303 ENCFF613LOW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHV/summary/ENCFF613LOW.w5 128 32 2.0 mean 1303 CHIP:H3K36me3:129 G1E +1304 ENCFF601MZE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHW/summary/ENCFF601MZE.w5 128 32 2.0 mean 1304 CHIP:H3K36me3:B10.H-2aH-4bp/Wts CH12.LX +1305 ENCFF541KFF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHX/summary/ENCFF541KFF.w5 128 32 2.0 mean 1305 CHIP:H3K27me3:129 G1E +1306 ENCFF923MXW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHY/summary/ENCFF923MXW.w5 128 32 2.0 mean 1306 CHIP:H3K27me3:B10.H-2aH-4bp/Wts CH12.LX +1307 ENCFF398WUM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DHZ/summary/ENCFF398WUM.w5 128 32 2.0 mean 1307 CHIP:POLR2AphosphoS5:DBA/2 MEL cell line +1308 ENCFF302RFZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIA/summary/ENCFF302RFZ.w5 128 32 2.0 mean 1308 CHIP:TAL1:DBA/2 MEL cell line +1309 ENCFF860JAB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIC/summary/ENCFF860JAB.w5 128 32 2.0 mean 1309 CHIP:GATA1:129 G1E +1310 ENCFF367IMF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DID/summary/ENCFF367IMF.w5 128 32 2.0 mean 1310 CHIP:GATA2:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1311 ENCFF630HUU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIE/summary/ENCFF630HUU.w5 128 32 2.0 mean 1311 CHIP:GATA2:129 G1E +1312 ENCFF754BDS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIF/summary/ENCFF754BDS.w5 128 32 2.0 mean 1312 CHIP:POLR2AphosphoS5:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1313 ENCFF561RBC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIG/summary/ENCFF561RBC.w5 128 32 2.0 mean 1313 CHIP:POLR2AphosphoS5:129 G1E +1314 ENCFF636WAD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIH/summary/ENCFF636WAD.w5 128 32 2.0 mean 1314 CHIP:PAX5:B10.H-2aH-4bp/Wts CH12.LX +1315 ENCFF779AOL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIL/summary/ENCFF779AOL.w5 128 32 2.0 mean 1315 CHIP:GATA1:CD-1 erythroblast embryo (14.5 days) +1316 ENCFF653ZIY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIM/summary/ENCFF653ZIY.w5 128 32 2.0 mean 1316 CHIP:TAL1:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1317 ENCFF263FFV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIN/summary/ENCFF263FFV.w5 128 32 2.0 mean 1317 CHIP:TAL1:129 G1E +1318 ENCFF498RZJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIP/summary/ENCFF498RZJ.w5 128 32 2.0 mean 1318 CHIP:CTCF:DBA/2 MEL cell line +1319 ENCFF279GQJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIQ/summary/ENCFF279GQJ.w5 128 32 2.0 mean 1319 CHIP:GATA1:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1320 ENCFF816XFR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIR/summary/ENCFF816XFR.w5 128 32 2.0 mean 1320 CHIP:CTCF:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1321 ENCFF938UFC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIS/summary/ENCFF938UFC.w5 128 32 2.0 mean 1321 CHIP:CTCF:129 G1E +1322 ENCFF844EOO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIU/summary/ENCFF844EOO.w5 128 32 2.0 mean 1322 CHIP:CTCF:B10.H-2aH-4bp/Wts CH12.LX +1323 ENCFF299BAW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIW/summary/ENCFF299BAW.w5 128 32 2.0 mean 1323 CHIP:H3K4me3:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1324 ENCFF249XCU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIX/summary/ENCFF249XCU.w5 128 32 2.0 mean 1324 CHIP:H3K4me3:129 G1E +1325 ENCFF469EMZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIY/summary/ENCFF469EMZ.w5 128 32 2.0 mean 1325 CHIP:H3K4me1:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1326 ENCFF999SUS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DIZ/summary/ENCFF999SUS.w5 128 32 2.0 mean 1326 CHIP:H3K27me3:129 G1E-ER4 treated with 10 nM 17B-estradiol for 24 hours +1327 ENCFF289VIM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000DJB/summary/ENCFF289VIM.w5 128 32 2.0 mean 1327 CHIP:H3K4me1:129 G1E +1328 ENCFF365FLT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQO/summary/ENCFF365FLT.w5 128 32 2.0 mean 1328 CHIP:ZNF384:B10.H-2aH-4bp/Wts CH12.LX +1329 ENCFF133UFU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQP/summary/ENCFF133UFU.w5 128 32 2.0 mean 1329 CHIP:ZMIZ1:B10.H-2aH-4bp/Wts CH12.LX +1330 ENCFF781WYP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQR/summary/ENCFF781WYP.w5 128 32 2.0 mean 1330 CHIP:HCFC1:B10.H-2aH-4bp/Wts CH12.LX +1331 ENCFF985RMX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQS/summary/ENCFF985RMX.w5 128 32 2.0 mean 1331 CHIP:GABPA:B10.H-2aH-4bp/Wts CH12.LX +1332 ENCFF283POK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQT/summary/ENCFF283POK.w5 128 32 2.0 mean 1332 CHIP:MAZ:B10.H-2aH-4bp/Wts CH12.LX +1333 ENCFF835AUM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQU/summary/ENCFF835AUM.w5 128 32 2.0 mean 1333 CHIP:KAT2A:B10.H-2aH-4bp/Wts CH12.LX +1334 ENCFF217FQC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQV/summary/ENCFF217FQC.w5 128 32 2.0 mean 1334 CHIP:CHD1:B10.H-2aH-4bp/Wts CH12.LX +1335 ENCFF411YYG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQW/summary/ENCFF411YYG.w5 128 32 2.0 mean 1335 CHIP:ZKSCAN1:B10.H-2aH-4bp/Wts CH12.LX +1336 ENCFF950EEV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQX/summary/ENCFF950EEV.w5 128 32 2.0 mean 1336 CHIP:UBTF:B10.H-2aH-4bp/Wts CH12.LX +1337 ENCFF659WQU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQY/summary/ENCFF659WQU.w5 128 32 2.0 mean 1337 CHIP:SIN3A:B10.H-2aH-4bp/Wts CH12.LX +1338 ENCFF210EXT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EQZ/summary/ENCFF210EXT.w5 128 32 2.0 mean 1338 CHIP:RCOR1:B10.H-2aH-4bp/Wts CH12.LX +1339 ENCFF165JVA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERA/summary/ENCFF165JVA.w5 128 32 2.0 mean 1339 CHIP:ETS1:B10.H-2aH-4bp/Wts CH12.LX +1340 ENCFF727IMP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERB/summary/ENCFF727IMP.w5 128 32 2.0 mean 1340 CHIP:MAFK:B10.H-2aH-4bp/Wts CH12.LX +1341 ENCFF668KLU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERC/summary/ENCFF668KLU.w5 128 32 2.0 mean 1341 CHIP:BHLHE40:B10.H-2aH-4bp/Wts CH12.LX +1342 ENCFF775LKP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERD/summary/ENCFF775LKP.w5 128 32 2.0 mean 1342 CHIP:NELFE:B10.H-2aH-4bp/Wts CH12.LX +1343 ENCFF724BKJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERE/summary/ENCFF724BKJ.w5 128 32 2.0 mean 1343 CHIP:MXI1:B10.H-2aH-4bp/Wts CH12.LX +1344 ENCFF216JRQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERG/summary/ENCFF216JRQ.w5 128 32 2.0 mean 1344 CHIP:SMC3:B10.H-2aH-4bp/Wts CH12.LX +1345 ENCFF630JDA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERH/summary/ENCFF630JDA.w5 128 32 2.0 mean 1345 CHIP:POLR2AphosphoS2:B10.H-2aH-4bp/Wts CH12.LX +1346 ENCFF140YUU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERI/summary/ENCFF140YUU.w5 128 32 2.0 mean 1346 CHIP:EP300:B10.H-2aH-4bp/Wts CH12.LX +1347 ENCFF495UJH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERJ/summary/ENCFF495UJH.w5 128 32 2.0 mean 1347 CHIP:USF2:B10.H-2aH-4bp/Wts CH12.LX +1348 ENCFF388SYO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERK/summary/ENCFF388SYO.w5 128 32 2.0 mean 1348 CHIP:RAD21:B10.H-2aH-4bp/Wts CH12.LX +1349 ENCFF291HYO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERL/summary/ENCFF291HYO.w5 128 32 2.0 mean 1349 CHIP:MAX:B10.H-2aH-4bp/Wts CH12.LX +1350 ENCFF025UEN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERM/summary/ENCFF025UEN.w5 128 32 2.0 mean 1350 CHIP:CTCF:B10.H-2aH-4bp/Wts CH12.LX +1351 ENCFF562UOS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERN/summary/ENCFF562UOS.w5 128 32 2.0 mean 1351 CHIP:MYC:B10.H-2aH-4bp/Wts CH12.LX +1352 ENCFF944MUS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERO/summary/ENCFF944MUS.w5 128 32 2.0 mean 1352 CHIP:JUN:B10.H-2aH-4bp/Wts CH12.LX +1353 ENCFF111ZPI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERP/summary/ENCFF111ZPI.w5 128 32 2.0 mean 1353 CHIP:TBP:B10.H-2aH-4bp/Wts CH12.LX +1354 ENCFF847BNC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERQ/summary/ENCFF847BNC.w5 128 32 2.0 mean 1354 CHIP:POLR2A:B10.H-2aH-4bp/Wts CH12.LX +1355 ENCFF544VSI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERR/summary/ENCFF544VSI.w5 128 32 2.0 mean 1355 CHIP:JUND:B10.H-2aH-4bp/Wts CH12.LX +1356 ENCFF162FEM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERU/summary/ENCFF162FEM.w5 128 32 2.0 mean 1356 CHIP:E2F4:B10.H-2aH-4bp/Wts CH12.LX +1357 ENCFF643WMY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERV/summary/ENCFF643WMY.w5 128 32 2.0 mean 1357 CHIP:ZNF384:129 ES-E14 +1358 ENCFF122FYP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ERX/summary/ENCFF122FYP.w5 128 32 2.0 mean 1358 CHIP:HCFC1:129 ES-E14 +1359 ENCFF807HIG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESD/summary/ENCFF807HIG.w5 128 32 2.0 mean 1359 CHIP:ZNF384:DBA/2 MEL cell line +1360 ENCFF689AFL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESE/summary/ENCFF689AFL.w5 128 32 2.0 mean 1360 CHIP:ZMIZ1:DBA/2 MEL cell line +1361 ENCFF707FPY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESG/summary/ENCFF707FPY.w5 128 32 2.0 mean 1361 CHIP:HCFC1:DBA/2 MEL cell line +1362 ENCFF252OTG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESH/summary/ENCFF252OTG.w5 128 32 2.0 mean 1362 CHIP:BHLHE40:DBA/2 MEL cell line +1363 ENCFF525ZGM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESI/summary/ENCFF525ZGM.w5 128 32 2.0 mean 1363 CHIP:RCOR1:DBA/2 MEL cell line +1364 ENCFF790OHZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESJ/summary/ENCFF790OHZ.w5 128 32 2.0 mean 1364 CHIP:UBTF:DBA/2 MEL cell line +1365 ENCFF104SUM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESK/summary/ENCFF104SUM.w5 128 32 2.0 mean 1365 CHIP:GABPA:DBA/2 MEL cell line +1366 ENCFF591TEI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESL/summary/ENCFF591TEI.w5 128 32 2.0 mean 1366 CHIP:MAZ:DBA/2 MEL cell line +1367 ENCFF013LGH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESM/summary/ENCFF013LGH.w5 128 32 2.0 mean 1367 CHIP:KAT2A:DBA/2 MEL cell line +1368 ENCFF498FCD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESN/summary/ENCFF498FCD.w5 128 32 2.0 mean 1368 CHIP:CHD1:DBA/2 MEL cell line +1369 ENCFF585YOH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESX/summary/ENCFF585YOH.w5 128 32 2.0 mean 1369 CHIP:ZKSCAN1:DBA/2 MEL cell line +1370 ENCFF369XQN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ESY/summary/ENCFF369XQN.w5 128 32 2.0 mean 1370 CHIP:MAFK:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1371 ENCFF283VEC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETA/summary/ENCFF283VEC.w5 128 32 2.0 mean 1371 CHIP:GATA1:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1372 ENCFF760BIB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETB/summary/ENCFF760BIB.w5 128 32 2.0 mean 1372 CHIP:ETS1:DBA/2 MEL cell line +1373 ENCFF297ZST /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETC/summary/ENCFF297ZST.w5 128 32 2.0 mean 1373 CHIP:SIN3A:DBA/2 MEL cell line +1374 ENCFF056UBA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETE/summary/ENCFF056UBA.w5 128 32 2.0 mean 1374 CHIP:CTCF:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1375 ENCFF141IPU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETF/summary/ENCFF141IPU.w5 128 32 2.0 mean 1375 CHIP:USF2:DBA/2 MEL cell line +1376 ENCFF128VVT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETG/summary/ENCFF128VVT.w5 128 32 2.0 mean 1376 CHIP:POLR2A:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1377 ENCFF516ABO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETK/summary/ENCFF516ABO.w5 128 32 2.0 mean 1377 CHIP:MAFK:DBA/2 MEL cell line +1378 ENCFF034BBD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETL/summary/ENCFF034BBD.w5 128 32 2.0 mean 1378 CHIP:SMC3:DBA/2 MEL cell line +1379 ENCFF587NFU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETM/summary/ENCFF587NFU.w5 128 32 2.0 mean 1379 CHIP:POLR2AphosphoS2:DBA/2 MEL cell line +1380 ENCFF780AWC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETN/summary/ENCFF780AWC.w5 128 32 2.0 mean 1380 CHIP:MXI1:DBA/2 MEL cell line +1381 ENCFF266YOT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETP/summary/ENCFF266YOT.w5 128 32 2.0 mean 1381 CHIP:EP300:DBA/2 MEL cell line +1382 ENCFF515BPN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETQ/summary/ENCFF515BPN.w5 128 32 2.0 mean 1382 CHIP:CTCF:DBA/2 MEL cell line +1383 ENCFF428NKW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETR/summary/ENCFF428NKW.w5 128 32 2.0 mean 1383 CHIP:MYB:DBA/2 MEL cell line +1384 ENCFF198FKD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETS/summary/ENCFF198FKD.w5 128 32 2.0 mean 1384 CHIP:RAD21:DBA/2 MEL cell line +1385 ENCFF527GUY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETT/summary/ENCFF527GUY.w5 128 32 2.0 mean 1385 CHIP:RAD21:DBA/2 MEL cell line treated with 2% dimethyl sulfoxide for 5 days +1386 ENCFF060EGQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETU/summary/ENCFF060EGQ.w5 128 32 2.0 mean 1386 CHIP:NELFE:DBA/2 MEL cell line +1387 ENCFF325EHX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETV/summary/ENCFF325EHX.w5 128 32 2.0 mean 1387 CHIP:EP300:DBA/2 MEL cell line +1388 ENCFF465SVV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETW/summary/ENCFF465SVV.w5 128 32 2.0 mean 1388 CHIP:USF2:DBA/2 MEL cell line +1389 ENCFF368ANL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETX/summary/ENCFF368ANL.w5 128 32 2.0 mean 1389 CHIP:MAX:DBA/2 MEL cell line +1390 ENCFF240ORP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETY/summary/ENCFF240ORP.w5 128 32 2.0 mean 1390 CHIP:E2F4:DBA/2 MEL cell line +1391 ENCFF673UJE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000ETZ/summary/ENCFF673UJE.w5 128 32 2.0 mean 1391 CHIP:JUND:DBA/2 MEL cell line +1392 ENCFF998KIS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EUA/summary/ENCFF998KIS.w5 128 32 2.0 mean 1392 CHIP:MYC:DBA/2 MEL cell line +1393 ENCFF026AMD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EUB/summary/ENCFF026AMD.w5 128 32 2.0 mean 1393 CHIP:TBP:DBA/2 MEL cell line +1394 ENCFF906BFI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EUC/summary/ENCFF906BFI.w5 128 32 2.0 mean 1394 CHIP:POLR2A:DBA/2 MEL cell line +1395 ENCFF160HQN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR000EUG/summary/ENCFF160HQN.w5 128 32 2.0 mean 1395 CHIP:GATA1:DBA/2 MEL cell line +1396 ENCFF661SPC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR002ZAG/summary/ENCFF661SPC.w5 128 32 2.0 mean 1396 CHIP:CTCF:C57BL/6 intestine postnatal (0 days) +1397 ENCFF409BJZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR007XTC/summary/ENCFF409BJZ.w5 128 32 2.0 mean 1397 CHIP:H3K9me3:C57BL/6 heart embryo (14.5 days) +1398 ENCFF672JMP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR008WOQ/summary/ENCFF672JMP.w5 128 32 2.0 mean 1398 CHIP:H3K27me3:C57BL/6 embryonic facial prominence embryo (13.5 days) +1399 ENCFF774BPM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR014MXQ/summary/ENCFF774BPM.w5 128 32 2.0 mean 1399 CHIP:H3K4me1:C57BL/6 hindbrain embryo (12.5 days) +1400 ENCFF212XYE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR014TEJ/summary/ENCFF212XYE.w5 128 32 2.0 mean 1400 CHIP:H3K9ac:C57BL/6 forebrain embryo (16.5 days) +1401 ENCFF396TSB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR014YAY/summary/ENCFF396TSB.w5 128 32 2.0 mean 1401 CHIP:H3K27me3:C57BL/6 intestine embryo (14.5 days) +1402 ENCFF538TEQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR021ALF/summary/ENCFF538TEQ.w5 128 32 2.0 mean 1402 CHIP:H3K27ac:C57BL/6 limb embryo (14.5 days) +1403 ENCFF577WZP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR022DED/summary/ENCFF577WZP.w5 128 32 2.0 mean 1403 CHIP:H3K9me3:C57BL/6 limb embryo (13.5 days) +1404 ENCFF469CPH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR022KDE/summary/ENCFF469CPH.w5 128 32 2.0 mean 1404 CHIP:H3K4me3:C57BL/6 forebrain embryo (15.5 days) +1405 ENCFF280VOA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR023VJO/summary/ENCFF280VOA.w5 128 32 2.0 mean 1405 CHIP:H3K4me3:C57BL/6 stomach embryo (14.5 days) +1406 ENCFF210YRR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR025AOC/summary/ENCFF210YRR.w5 128 32 2.0 mean 1406 CHIP:H3K27me3:C57BL/6 lung postnatal (0 days) +1407 ENCFF786GEI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR027DMG/summary/ENCFF786GEI.w5 128 32 2.0 mean 1407 CHIP:H3K36me3:C57BL/6 embryonic facial prominence embryo (11.5 days) +1408 ENCFF379BOF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR028VCU/summary/ENCFF379BOF.w5 128 32 2.0 mean 1408 CHIP:H3K9ac:C57BL/6 midbrain postnatal (0 days) +1409 ENCFF367TZB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR028ZHS/summary/ENCFF367TZB.w5 128 32 2.0 mean 1409 CHIP:H3K9me3:C57BL/6 limb embryo (15.5 days) +1410 ENCFF043LTY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR032JUI/summary/ENCFF043LTY.w5 128 32 2.0 mean 1410 CHIP:H3K4me1:129 E14TG2a.4 +1411 ENCFF507ODK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR033OWC/summary/ENCFF507ODK.w5 128 32 2.0 mean 1411 CHIP:ELF1:DBA/2 MEL cell line +1412 ENCFF348ZCL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR036YKL/summary/ENCFF348ZCL.w5 128 32 2.0 mean 1412 CHIP:H3K4me2:C57BL/6 kidney embryo (15.5 days) +1413 ENCFF813MON /home/drk/tillage/datasets/mouse/chip/encode/ENCSR037HCS/summary/ENCFF813MON.w5 128 32 2.0 mean 1413 CHIP:H3K36me3:C57BL/6 liver embryo (13.5 days) +1414 ENCFF044DZV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR037HLB/summary/ENCFF044DZV.w5 128 32 2.0 mean 1414 CHIP:H3K4me1:C57BL/6 midbrain embryo (14.5 days) +1415 ENCFF101ASP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR041KEJ/summary/ENCFF101ASP.w5 128 32 2.0 mean 1415 CHIP:H3K9me3:C57BL/6 forebrain embryo (13.5 days) +1416 ENCFF186QKQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR041SMK/summary/ENCFF186QKQ.w5 128 32 2.0 mean 1416 CHIP:CTCF:C57BL/6 liver postnatal (0 days) +1417 ENCFF030BTL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR044SNE/summary/ENCFF030BTL.w5 128 32 2.0 mean 1417 CHIP:H3K4me3:C57BL/6 neural tube embryo (15.5 days) +1418 ENCFF849CQA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR044SUW/summary/ENCFF849CQA.w5 128 32 2.0 mean 1418 CHIP:H3K4me2:C57BL/6 forebrain embryo (13.5 days) +1419 ENCFF419CPS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR045NOD/summary/ENCFF419CPS.w5 128 32 2.0 mean 1419 CHIP:H3K4me1:C57BL/6 liver embryo (13.5 days) +1420 ENCFF574LGA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR046SWI/summary/ENCFF574LGA.w5 128 32 2.0 mean 1420 CHIP:H3K27me3:C57BL/6 hindbrain embryo (16.5 days) +1421 ENCFF563JNZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR048IZJ/summary/ENCFF563JNZ.w5 128 32 2.0 mean 1421 CHIP:H3K9ac:C57BL/6 stomach postnatal (0 days) +1422 ENCFF887SQZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR051CUH/summary/ENCFF887SQZ.w5 128 32 2.0 mean 1422 CHIP:H3K4me1:C57BL/6 intestine embryo (15.5 days) +1423 ENCFF774GGS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR052CDF/summary/ENCFF774GGS.w5 128 32 2.0 mean 1423 CHIP:H3K4me3:C57BL/6 heart embryo (14.5 days) +1424 ENCFF774AQE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR054JHZ/summary/ENCFF774AQE.w5 128 32 2.0 mean 1424 CHIP:H3K27ac:C57BL/6 hindbrain embryo (14.5 days) +1425 ENCFF394ABQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR057BKH/summary/ENCFF394ABQ.w5 128 32 2.0 mean 1425 CHIP:H3K4me3:C57BL/6 embryonic facial prominence embryo (13.5 days) +1426 ENCFF298GLI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR057SHA/summary/ENCFF298GLI.w5 128 32 2.0 mean 1426 CHIP:H3K27ac:C57BL/6 kidney embryo (14.5 days) +1427 ENCFF274AWM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR058DOA/summary/ENCFF274AWM.w5 128 32 2.0 mean 1427 CHIP:H3K27ac:C57BL/6 liver embryo (11.5 days) +1428 ENCFF312WJP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR059LYY/summary/ENCFF312WJP.w5 128 32 2.0 mean 1428 CHIP:H3K4me3:C57BL/6 embryonic facial prominence embryo (14.5 days) +1429 ENCFF012GHA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR059MBO/summary/ENCFF012GHA.w5 128 32 2.0 mean 1429 CHIP:H3K27me3:129 E14TG2a.4 +1430 ENCFF944UBT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR061DPP/summary/ENCFF944UBT.w5 128 32 2.0 mean 1430 CHIP:H3K27me3:C57BL/6 embryonic facial prominence embryo (15.5 days) +1431 ENCFF518FTX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR064DGY/summary/ENCFF518FTX.w5 128 32 2.0 mean 1431 CHIP:H3K27me3:C57BL/6 stomach embryo (14.5 days) +1432 ENCFF999AED /home/drk/tillage/datasets/mouse/chip/encode/ENCSR065CJC/summary/ENCFF999AED.w5 128 32 2.0 mean 1432 CHIP:H3K9ac:C57BL/6 neural tube embryo (12.5 days) +1433 ENCFF887HCS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR065LAB/summary/ENCFF887HCS.w5 128 32 2.0 mean 1433 CHIP:H3K9me3:C57BL/6 midbrain postnatal (0 days) +1434 ENCFF985XJA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR066LZB/summary/ENCFF985XJA.w5 128 32 2.0 mean 1434 CHIP:H3K36me3:C57BL/6 forebrain embryo (11.5 days) +1435 ENCFF652HPR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR066WUD/summary/ENCFF652HPR.w5 128 32 2.0 mean 1435 CHIP:H3K36me3:C57BL/6 midbrain embryo (13.5 days) +1436 ENCFF121XJR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR066XFL/summary/ENCFF121XJR.w5 128 32 2.0 mean 1436 CHIP:H3K27ac:C57BL/6 hindbrain embryo (15.5 days) +1437 ENCFF371WPS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR066XXZ/summary/ENCFF371WPS.w5 128 32 2.0 mean 1437 CHIP:H3K36me3:C57BL/6 hindbrain embryo (14.5 days) +1438 ENCFF537ZRP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR067FKP/summary/ENCFF537ZRP.w5 128 32 2.0 mean 1438 CHIP:H3K9ac:C57BL/6 midbrain embryo (14.5 days) +1439 ENCFF880WPO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR067ZDE/summary/ENCFF880WPO.w5 128 32 2.0 mean 1439 CHIP:H3K4me2:C57BL/6 forebrain embryo (11.5 days) +1440 ENCFF565CYY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR068XYW/summary/ENCFF565CYY.w5 128 32 2.0 mean 1440 CHIP:H3K9ac:C57BL/6 midbrain embryo (16.5 days) +1441 ENCFF606CKV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR069TDC/summary/ENCFF606CKV.w5 128 32 2.0 mean 1441 CHIP:H3K36me3:C57BL/6 forebrain postnatal (0 days) +1442 ENCFF045OSV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR069XHI/summary/ENCFF045OSV.w5 128 32 2.0 mean 1442 CHIP:H3K9ac:C57BL/6 heart embryo (13.5 days) +1443 ENCFF183CXT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR070MOK/summary/ENCFF183CXT.w5 128 32 2.0 mean 1443 CHIP:H3K27me3:C57BL/6 forebrain postnatal (0 days) +1444 ENCFF921YZN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR071SQK/summary/ENCFF921YZN.w5 128 32 2.0 mean 1444 CHIP:H3K9me3:C57BL/6 heart embryo (15.5 days) +1445 ENCFF518VSR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR075SNV/summary/ENCFF518VSR.w5 128 32 2.0 mean 1445 CHIP:H3K27ac:C57BL/6 liver embryo (14.5 days) +1446 ENCFF170JVA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR076FAM/summary/ENCFF170JVA.w5 128 32 2.0 mean 1446 CHIP:H3K9ac:C57BL/6 embryonic facial prominence embryo (11.5 days) +1447 ENCFF592XTS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR076MXH/summary/ENCFF592XTS.w5 128 32 2.0 mean 1447 CHIP:H3K4me2:C57BL/6 stomach embryo (14.5 days) +1448 ENCFF730VFB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR080GQM/summary/ENCFF730VFB.w5 128 32 2.0 mean 1448 CHIP:H3K4me1:C57BL/6 heart embryo (14.5 days) +1449 ENCFF731BDW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR085EYQ/summary/ENCFF731BDW.w5 128 32 2.0 mean 1449 CHIP:H3K27me3:C57BL/6 limb embryo (11.5 days) +1450 ENCFF654YXS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR087JEN/summary/ENCFF654YXS.w5 128 32 2.0 mean 1450 CHIP:H3K36me3:C57BL/6 forebrain embryo (13.5 days) +1451 ENCFF290BIA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR087PLZ/summary/ENCFF290BIA.w5 128 32 2.0 mean 1451 CHIP:H3K9ac:C57BL/6 neural tube embryo (13.5 days) +1452 ENCFF230FQZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR088UKA/summary/ENCFF230FQZ.w5 128 32 2.0 mean 1452 CHIP:H3K27ac:C57BL/6 midbrain embryo (11.5 days) +1453 ENCFF633MDI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR091WNX/summary/ENCFF633MDI.w5 128 32 2.0 mean 1453 CHIP:H3K4me1:C57BL/6 embryonic facial prominence embryo (15.5 days) +1454 ENCFF229GJB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR093BYV/summary/ENCFF229GJB.w5 128 32 2.0 mean 1454 CHIP:H3K4me3:C57BL/6 neural tube embryo (14.5 days) +1455 ENCFF114FKU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR093DWU/summary/ENCFF114FKU.w5 128 32 2.0 mean 1455 CHIP:H3K9me3:C57BL/6 forebrain postnatal (0 days) +1456 ENCFF846FSQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR094QZC/summary/ENCFF846FSQ.w5 128 32 2.0 mean 1456 CHIP:H3K36me3:C57BL/6 neural tube embryo (12.5 days) +1457 ENCFF835DLZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR094TTT/summary/ENCFF835DLZ.w5 128 32 2.0 mean 1457 CHIP:H3K27ac:C57BL/6 forebrain postnatal (0 days) +1458 ENCFF947IGN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR095FDG/summary/ENCFF947IGN.w5 128 32 2.0 mean 1458 CHIP:H3K9me3:C57BL/6 liver embryo (16.5 days) +1459 ENCFF069MRV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR098AHF/summary/ENCFF069MRV.w5 128 32 2.0 mean 1459 CHIP:H3K4me2:C57BL/6 limb embryo (15.5 days) +1460 ENCFF637INN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR098USP/summary/ENCFF637INN.w5 128 32 2.0 mean 1460 CHIP:H3K9me3:C57BL/6 heart embryo (13.5 days) +1461 ENCFF223PHS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR099BYW/summary/ENCFF223PHS.w5 128 32 2.0 mean 1461 CHIP:H3K27me3:C57BL/6 neural tube embryo (14.5 days) +1462 ENCFF854ASW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR100DLL/summary/ENCFF854ASW.w5 128 32 2.0 mean 1462 CHIP:H3K4me2:C57BL/6 intestine embryo (16.5 days) +1463 ENCFF612RDE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR104PWP/summary/ENCFF612RDE.w5 128 32 2.0 mean 1463 CHIP:H3K27me3:C57BL/6 midbrain embryo (12.5 days) +1464 ENCFF685EPG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR104QEN/summary/ENCFF685EPG.w5 128 32 2.0 mean 1464 CHIP:CTCF:C57BL/6 stomach postnatal (0 days) +1465 ENCFF499LGL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR105OGF/summary/ENCFF499LGL.w5 128 32 2.0 mean 1465 CHIP:H3K9ac:C57BL/6 embryonic facial prominence embryo (12.5 days) +1466 ENCFF508WCS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR106QSU/summary/ENCFF508WCS.w5 128 32 2.0 mean 1466 CHIP:H3K4me3:C57BL/6 embryonic facial prominence embryo (12.5 days) +1467 ENCFF032KOM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR107SLP/summary/ENCFF032KOM.w5 128 32 2.0 mean 1467 CHIP:H3K36me3:C57BL/6 neural tube embryo (13.5 days) +1468 ENCFF118BRC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR108TWE/summary/ENCFF118BRC.w5 128 32 2.0 mean 1468 CHIP:H3K36me3:C57BL/6 lung embryo (14.5 days) +1469 ENCFF899RFO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR110MSZ/summary/ENCFF899RFO.w5 128 32 2.0 mean 1469 CHIP:H3K4me2:C57BL/6 liver embryo (12.5 days) +1470 ENCFF959NHK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR110TIW/summary/ENCFF959NHK.w5 128 32 2.0 mean 1470 CHIP:H3K4me3:C57BL/6 hindbrain embryo (16.5 days) +1471 ENCFF061QXI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR115FTP/summary/ENCFF061QXI.w5 128 32 2.0 mean 1471 CHIP:H3K4me2:C57BL/6 limb embryo (11.5 days) +1472 ENCFF808VAT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR119YTR/summary/ENCFF808VAT.w5 128 32 2.0 mean 1472 CHIP:H3K4me3:C57BL/6 heart embryo (16.5 days) +1473 ENCFF069GVS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR121BWA/summary/ENCFF069GVS.w5 128 32 2.0 mean 1473 CHIP:H3K36me3:C57BL/6 kidney embryo (16.5 days) +1474 ENCFF637DCW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR122CJZ/summary/ENCFF637DCW.w5 128 32 2.0 mean 1474 CHIP:H3K9me3:C57BL/6 heart embryo (16.5 days) +1475 ENCFF379MVJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR122HLY/summary/ENCFF379MVJ.w5 128 32 2.0 mean 1475 CHIP:H3K27me3:C57BL/6 heart embryo (12.5 days) +1476 ENCFF937AXD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR123MLY/summary/ENCFF937AXD.w5 128 32 2.0 mean 1476 CHIP:H3K27ac:C57BL/6 heart embryo (12.5 days) +1477 ENCFF716TGN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR125VVG/summary/ENCFF716TGN.w5 128 32 2.0 mean 1477 CHIP:H3K9me3:C57BL/6 liver embryo (14.5 days) +1478 ENCFF719KVF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR128ZCB/summary/ENCFF719KVF.w5 128 32 2.0 mean 1478 CHIP:H3K9ac:C57BL/6 forebrain embryo (14.5 days) +1479 ENCFF041JZL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR129DIK/summary/ENCFF041JZL.w5 128 32 2.0 mean 1479 CHIP:H3K4me3:C57BL/6 forebrain embryo (16.5 days) +1480 ENCFF177SVC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR129LAP/summary/ENCFF177SVC.w5 128 32 2.0 mean 1480 CHIP:H3K27ac:C57BL/6 hindbrain embryo (11.5 days) +1481 ENCFF610HBD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR129OJN/summary/ENCFF610HBD.w5 128 32 2.0 mean 1481 CHIP:H3K27me3:C57BL/6 midbrain embryo (13.5 days) +1482 ENCFF909TOQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR133EGP/summary/ENCFF909TOQ.w5 128 32 2.0 mean 1482 CHIP:H3K4me1:C57BL/6 liver embryo (15.5 days) +1483 ENCFF943PON /home/drk/tillage/datasets/mouse/chip/encode/ENCSR135QMP/summary/ENCFF943PON.w5 128 32 2.0 mean 1483 CHIP:H3K27me3:C57BL/6 liver embryo (16.5 days) +1484 ENCFF623PQH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR135SWH/summary/ENCFF623PQH.w5 128 32 2.0 mean 1484 CHIP:NRF1:DBA/2 MEL cell line +1485 ENCFF285ZJD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR136GMT/summary/ENCFF285ZJD.w5 128 32 2.0 mean 1485 CHIP:H3K27ac:C57BL/6 liver embryo (12.5 days) +1486 ENCFF820QKT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR137NUN/summary/ENCFF820QKT.w5 128 32 2.0 mean 1486 CHIP:H3K9me3:C57BL/6 embryonic facial prominence embryo (15.5 days) +1487 ENCFF681GAF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR140UEX/summary/ENCFF681GAF.w5 128 32 2.0 mean 1487 CHIP:H3K27ac:C57BL/6 lung embryo (16.5 days) +1488 ENCFF873EBR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR140YPL/summary/ENCFF873EBR.w5 128 32 2.0 mean 1488 CHIP:H3K27ac:C57BL/6 kidney postnatal (0 days) +1489 ENCFF033MMS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR141ZQF/summary/ENCFF033MMS.w5 128 32 2.0 mean 1489 CHIP:H3K4me1:C57BL/6 forebrain embryo (16.5 days) +1490 ENCFF083ZQN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR143WOK/summary/ENCFF083ZQN.w5 128 32 2.0 mean 1490 CHIP:CTCF:C57BL/6 kidney postnatal (0 days) +1491 ENCFF421HSW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR147PYG/summary/ENCFF421HSW.w5 128 32 2.0 mean 1491 CHIP:H3K9me3:C57BL/6 embryonic facial prominence embryo (13.5 days) +1492 ENCFF164GUC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR148IGO/summary/ENCFF164GUC.w5 128 32 2.0 mean 1492 CHIP:H3K27me3:C57BL/6 lung embryo (14.5 days) +1493 ENCFF741LSB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR149GYK/summary/ENCFF741LSB.w5 128 32 2.0 mean 1493 CHIP:H3K9me3:C57BL/6 liver embryo (12.5 days) +1494 ENCFF251FHP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR150RGT/summary/ENCFF251FHP.w5 128 32 2.0 mean 1494 CHIP:CTCF:C57BL/6 hindbrain postnatal (0 days) +1495 ENCFF440LYR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR151APL/summary/ENCFF440LYR.w5 128 32 2.0 mean 1495 CHIP:H3K27ac:C57BL/6 embryonic facial prominence embryo (10.5 days) +1496 ENCFF957GWA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR154DTK/summary/ENCFF957GWA.w5 128 32 2.0 mean 1496 CHIP:H3K4me2:C57BL/6 lung embryo (16.5 days) +1497 ENCFF450IIR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR157IVC/summary/ENCFF450IIR.w5 128 32 2.0 mean 1497 CHIP:H3K4me1:C57BL/6 midbrain embryo (12.5 days) +1498 ENCFF173OSG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR157LYR/summary/ENCFF173OSG.w5 128 32 2.0 mean 1498 CHIP:H3K4me1:C57BL/6 intestine embryo (14.5 days) +1499 ENCFF493WPM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR158ONM/summary/ENCFF493WPM.w5 128 32 2.0 mean 1499 CHIP:H3K4me3:C57BL/6 hindbrain embryo (12.5 days) +1500 ENCFF028YVD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR159RVN/summary/ENCFF028YVD.w5 128 32 2.0 mean 1500 CHIP:H3K4me1:C57BL/6 intestine postnatal (0 days) +1501 ENCFF087LVF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR161DAW/summary/ENCFF087LVF.w5 128 32 2.0 mean 1501 CHIP:H3K4me2:C57BL/6 hindbrain embryo (16.5 days) +1502 ENCFF111SQJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR161UUY/summary/ENCFF111SQJ.w5 128 32 2.0 mean 1502 CHIP:H3K9ac:C57BL/6 forebrain embryo (12.5 days) +1503 ENCFF842FSB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR167ZGV/summary/ENCFF842FSB.w5 128 32 2.0 mean 1503 CHIP:H3K4me3:C57BL/6 midbrain embryo (13.5 days) +1504 ENCFF465QRZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR172XOZ/summary/ENCFF465QRZ.w5 128 32 2.0 mean 1504 CHIP:H3K4me3:C57BL/6 forebrain embryo (14.5 days) +1505 ENCFF289PYS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR175KBJ/summary/ENCFF289PYS.w5 128 32 2.0 mean 1505 CHIP:H3K27ac:C57BL/6 liver embryo (13.5 days) +1506 ENCFF480NZE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR175QZX/summary/ENCFF480NZE.w5 128 32 2.0 mean 1506 CHIP:H3K36me3:C57BL/6 hindbrain embryo (11.5 days) +1507 ENCFF994FKT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR176BXC/summary/ENCFF994FKT.w5 128 32 2.0 mean 1507 CHIP:H3K4me3:C57BL/6 limb embryo (14.5 days) +1508 ENCFF837LYE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR185JBL/summary/ENCFF837LYE.w5 128 32 2.0 mean 1508 CHIP:H3K4me3:C57BL/6 hindbrain embryo (14.5 days) +1509 ENCFF361RBA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR186PIV/summary/ENCFF361RBA.w5 128 32 2.0 mean 1509 CHIP:H3K9ac:C57BL/6 hindbrain embryo (14.5 days) +1510 ENCFF768XVB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR190RKJ/summary/ENCFF768XVB.w5 128 32 2.0 mean 1510 CHIP:H3K9ac:C57BL/6 hindbrain embryo (13.5 days) +1511 ENCFF258AAD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR191XHV/summary/ENCFF258AAD.w5 128 32 2.0 mean 1511 CHIP:H3K9me3:C57BL/6 liver embryo (13.5 days) +1512 ENCFF900GLU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR193AEW/summary/ENCFF900GLU.w5 128 32 2.0 mean 1512 CHIP:H3K4me2:C57BL/6 embryonic facial prominence embryo (15.5 days) +1513 ENCFF353ZBQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR194GNY/summary/ENCFF353ZBQ.w5 128 32 2.0 mean 1513 CHIP:GATA4:C57BL/6xSv129 liver adult +1514 ENCFF877WYE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR195NDO/summary/ENCFF877WYE.w5 128 32 2.0 mean 1514 CHIP:H3K4me2:C57BL/6 embryonic facial prominence embryo (12.5 days) +1515 ENCFF553YRO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR196ENU/summary/ENCFF553YRO.w5 128 32 2.0 mean 1515 CHIP:H3K4me1:C57BL/6 kidney embryo (14.5 days) +1516 ENCFF115TVW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR198ACZ/summary/ENCFF115TVW.w5 128 32 2.0 mean 1516 CHIP:H3K4me3:C57BL/6 intestine postnatal (0 days) +1517 ENCFF002MTC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR203KIB/summary/ENCFF002MTC.w5 128 32 2.0 mean 1517 CHIP:H3K4me3:C57BL/6 midbrain embryo (14.5 days) +1518 ENCFF692XLZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR205XBQ/summary/ENCFF692XLZ.w5 128 32 2.0 mean 1518 CHIP:H3K36me3:C57BL/6 midbrain embryo (16.5 days) +1519 ENCFF795DAU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR207UMX/summary/ENCFF795DAU.w5 128 32 2.0 mean 1519 CHIP:H3K36me3:C57BL/6 neural tube embryo (15.5 days) +1520 ENCFF469DBC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR212KGS/summary/ENCFF469DBC.w5 128 32 2.0 mean 1520 CHIP:H3K4me3:129 E14TG2a.4 +1521 ENCFF305IHU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR222IHX/summary/ENCFF305IHU.w5 128 32 2.0 mean 1521 CHIP:H3K27ac:C57BL/6 heart embryo (11.5 days) +1522 ENCFF705MSQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR223FDX/summary/ENCFF705MSQ.w5 128 32 2.0 mean 1522 CHIP:H3K9me3:C57BL/6 neural tube embryo (14.5 days) +1523 ENCFF563GBE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR227UTY/summary/ENCFF563GBE.w5 128 32 2.0 mean 1523 CHIP:H3K36me3:C57BL/6 forebrain embryo (14.5 days) +1524 ENCFF865VFL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR229LTY/summary/ENCFF865VFL.w5 128 32 2.0 mean 1524 CHIP:H3K27me3:C57BL/6 limb embryo (12.5 days) +1525 ENCFF755WDT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR231CHC/summary/ENCFF755WDT.w5 128 32 2.0 mean 1525 CHIP:H3K27me3:C57BL/6 limb embryo (15.5 days) +1526 ENCFF841DUP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR233LBT/summary/ENCFF841DUP.w5 128 32 2.0 mean 1526 CHIP:H3K36me3:C57BL/6 limb embryo (12.5 days) +1527 ENCFF263ROX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR234ISO/summary/ENCFF263ROX.w5 128 32 2.0 mean 1527 CHIP:H3K4me1:C57BL/6 liver embryo (14.5 days) +1528 ENCFF791DCG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR234YTN/summary/ENCFF791DCG.w5 128 32 2.0 mean 1528 CHIP:H3K4me2:C57BL/6 hindbrain embryo (14.5 days) +1529 ENCFF690EIB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR235JCY/summary/ENCFF690EIB.w5 128 32 2.0 mean 1529 CHIP:H3K36me3:C57BL/6 heart postnatal (0 days) +1530 ENCFF920CEX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR238SGC/summary/ENCFF920CEX.w5 128 32 2.0 mean 1530 CHIP:H3K4me1:C57BL/6 limb embryo (10.5 days) +1531 ENCFF399KQJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR238ZCJ/summary/ENCFF399KQJ.w5 128 32 2.0 mean 1531 CHIP:H3K9me3:C57BL/6 lung postnatal (0 days) +1532 ENCFF046KVG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR239TSZ/summary/ENCFF046KVG.w5 128 32 2.0 mean 1532 CHIP:H3K36me3:C57BL/6 heart embryo (13.5 days) +1533 ENCFF217EPP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR240OUM/summary/ENCFF217EPP.w5 128 32 2.0 mean 1533 CHIP:H3K27me3:C57BL/6 neural tube embryo (11.5 days) +1534 ENCFF789UMC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR241BSK/summary/ENCFF789UMC.w5 128 32 2.0 mean 1534 CHIP:H3K27ac:C57BL/6 neural tube embryo (15.5 days) +1535 ENCFF918CGY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR242PHH/summary/ENCFF918CGY.w5 128 32 2.0 mean 1535 CHIP:H3K36me3:C57BL/6 limb embryo (10.5 days) +1536 ENCFF193NMX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR243JOL/summary/ENCFF193NMX.w5 128 32 2.0 mean 1536 CHIP:H3K4me1:C57BL/6 forebrain embryo (12.5 days) +1537 ENCFF205JZO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR244ASF/summary/ENCFF205JZO.w5 128 32 2.0 mean 1537 CHIP:H3K4me3:C57BL/6 limb embryo (15.5 days) +1538 ENCFF800NSG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR244KCW/summary/ENCFF800NSG.w5 128 32 2.0 mean 1538 CHIP:H3K27me3:C57BL/6 liver embryo (11.5 days) +1539 ENCFF610GUY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR249AUA/summary/ENCFF610GUY.w5 128 32 2.0 mean 1539 CHIP:H3K9ac:C57BL/6 lung embryo (14.5 days) +1540 ENCFF165DVJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR250LXH/summary/ENCFF165DVJ.w5 128 32 2.0 mean 1540 CHIP:H3K36me3:C57BL/6 lung postnatal (0 days) +1541 ENCFF746ONG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR251LFV/summary/ENCFF746ONG.w5 128 32 2.0 mean 1541 CHIP:H3K4me1:C57BL/6 heart embryo (16.5 days) +1542 ENCFF315VST /home/drk/tillage/datasets/mouse/chip/encode/ENCSR252GKD/summary/ENCFF315VST.w5 128 32 2.0 mean 1542 CHIP:H3K4me3:C57BL/6 liver embryo (16.5 days) +1543 ENCFF406MDW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR252ONR/summary/ENCFF406MDW.w5 128 32 2.0 mean 1543 CHIP:H3K27ac:C57BL/6 midbrain embryo (12.5 days) +1544 ENCFF704PEM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR253IEG/summary/ENCFF704PEM.w5 128 32 2.0 mean 1544 CHIP:H3K4me1:C57BL/6 midbrain embryo (13.5 days) +1545 ENCFF785WPG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR253QPK/summary/ENCFF785WPG.w5 128 32 2.0 mean 1545 CHIP:H3K36me3:129 E14TG2a.4 +1546 ENCFF900XUW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR254AHA/summary/ENCFF900XUW.w5 128 32 2.0 mean 1546 CHIP:H3K27ac:C57BL/6 midbrain embryo (14.5 days) +1547 ENCFF983GFL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR257GTR/summary/ENCFF983GFL.w5 128 32 2.0 mean 1547 CHIP:H3K27me3:C57BL/6 embryonic facial prominence embryo (12.5 days) +1548 ENCFF667NCZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR257JSX/summary/ENCFF667NCZ.w5 128 32 2.0 mean 1548 CHIP:H3K4me1:C57BL/6 hindbrain embryo (16.5 days) +1549 ENCFF218NHY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR258AED/summary/ENCFF218NHY.w5 128 32 2.0 mean 1549 CHIP:H3K4me1:C57BL/6 embryonic facial prominence embryo (13.5 days) +1550 ENCFF755OHM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR258RGT/summary/ENCFF755OHM.w5 128 32 2.0 mean 1550 CHIP:H3K4me2:C57BL/6 liver embryo (15.5 days) +1551 ENCFF330NUS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR258YWW/summary/ENCFF330NUS.w5 128 32 2.0 mean 1551 CHIP:H3K4me3:C57BL/6 forebrain postnatal (0 days) +1552 ENCFF408PKX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR259KYK/summary/ENCFF408PKX.w5 128 32 2.0 mean 1552 CHIP:H3K27me3:C57BL/6 hindbrain embryo (15.5 days) +1553 ENCFF657UHZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR260OUP/summary/ENCFF657UHZ.w5 128 32 2.0 mean 1553 CHIP:H3K9ac:C57BL/6 intestine embryo (14.5 days) +1554 ENCFF770WCB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR261OAK/summary/ENCFF770WCB.w5 128 32 2.0 mean 1554 CHIP:H3K4me2:C57BL/6 midbrain embryo (11.5 days) +1555 ENCFF377ZXP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR262CSU/summary/ENCFF377ZXP.w5 128 32 2.0 mean 1555 CHIP:H3K4me3:C57BL/6 lung postnatal (0 days) +1556 ENCFF428RXK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR263CKR/summary/ENCFF428RXK.w5 128 32 2.0 mean 1556 CHIP:H3K4me1:C57BL/6 neural tube embryo (12.5 days) +1557 ENCFF849QJF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR264HHL/summary/ENCFF849QJF.w5 128 32 2.0 mean 1557 CHIP:H3K36me3:C57BL/6 limb embryo (15.5 days) +1558 ENCFF921KVA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR264TXI/summary/ENCFF921KVA.w5 128 32 2.0 mean 1558 CHIP:H3K4me2:C57BL/6 forebrain embryo (14.5 days) +1559 ENCFF494OOQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR265NBM/summary/ENCFF494OOQ.w5 128 32 2.0 mean 1559 CHIP:H3K27ac:C57BL/6 neural tube embryo (14.5 days) +1560 ENCFF046VWN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR266JQW/summary/ENCFF046VWN.w5 128 32 2.0 mean 1560 CHIP:H3K27me3:C57BL/6 heart embryo (10.5 days) +1561 ENCFF034URR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR270WWV/summary/ENCFF034URR.w5 128 32 2.0 mean 1561 CHIP:H3K9me3:C57BL/6 forebrain embryo (14.5 days) +1562 ENCFF853FDI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR272GNQ/summary/ENCFF853FDI.w5 128 32 2.0 mean 1562 CHIP:H3K4me1:C57BL/6 midbrain embryo (10.5 days) +1563 ENCFF353QFF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR272XPJ/summary/ENCFF353QFF.w5 128 32 2.0 mean 1563 CHIP:H3K36me3:C57BL/6 intestine embryo (16.5 days) +1564 ENCFF443SGX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR274ACJ/summary/ENCFF443SGX.w5 128 32 2.0 mean 1564 CHIP:H3K9ac:C57BL/6 limb embryo (14.5 days) +1565 ENCFF827WXG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR275KPI/summary/ENCFF827WXG.w5 128 32 2.0 mean 1565 CHIP:H3K27ac:C57BL/6 forebrain embryo (11.5 days) +1566 ENCFF886OPQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR282GAG/summary/ENCFF886OPQ.w5 128 32 2.0 mean 1566 CHIP:H3K27me3:C57BL/6 stomach embryo (15.5 days) +1567 ENCFF950JKI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR282OTI/summary/ENCFF950JKI.w5 128 32 2.0 mean 1567 CHIP:H3K4me2:C57BL/6 stomach embryo (16.5 days) +1568 ENCFF081AUZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR283RFW/summary/ENCFF081AUZ.w5 128 32 2.0 mean 1568 CHIP:H3K4me3:C57BL/6 midbrain embryo (11.5 days) +1569 ENCFF798NZC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR285IQN/summary/ENCFF798NZC.w5 128 32 2.0 mean 1569 CHIP:H3K27me3:C57BL/6 embryonic facial prominence embryo (10.5 days) +1570 ENCFF851ZPG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR286IGS/summary/ENCFF851ZPG.w5 128 32 2.0 mean 1570 CHIP:H3K9ac:C57BL/6 limb embryo (11.5 days) +1571 ENCFF147ZWY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR286OKN/summary/ENCFF147ZWY.w5 128 32 2.0 mean 1571 CHIP:H3K9ac:C57BL/6 midbrain embryo (13.5 days) +1572 ENCFF761AXJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR288LNF/summary/ENCFF761AXJ.w5 128 32 2.0 mean 1572 CHIP:H3K4me2:C57BL/6 stomach postnatal (0 days) +1573 ENCFF495TXX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR288OHO/summary/ENCFF495TXX.w5 128 32 2.0 mean 1573 CHIP:H3K9ac:C57BL/6 kidney postnatal (0 days) +1574 ENCFF066PYN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR289SWJ/summary/ENCFF066PYN.w5 128 32 2.0 mean 1574 CHIP:H3K27ac:C57BL/6 neural tube embryo (13.5 days) +1575 ENCFF613PHO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR293ORS/summary/ENCFF613PHO.w5 128 32 2.0 mean 1575 CHIP:H3K9ac:C57BL/6 stomach embryo (14.5 days) +1576 ENCFF600CWP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR293WTN/summary/ENCFF600CWP.w5 128 32 2.0 mean 1576 CHIP:ELF1:B10.H-2aH-4bp/Wts CH12.LX +1577 ENCFF389JEL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR295PFM/summary/ENCFF389JEL.w5 128 32 2.0 mean 1577 CHIP:H3K4me3:C57BL/6 lung embryo (16.5 days) +1578 ENCFF004EZJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR295ZLV/summary/ENCFF004EZJ.w5 128 32 2.0 mean 1578 CHIP:H3K36me3:C57BL/6 liver embryo (12.5 days) +1579 ENCFF597HKP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR297CHD/summary/ENCFF597HKP.w5 128 32 2.0 mean 1579 CHIP:H3K27me3:C57BL/6 forebrain embryo (12.5 days) +1580 ENCFF499LUF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR299DRH/summary/ENCFF499LUF.w5 128 32 2.0 mean 1580 CHIP:H3K9me3:C57BL/6 hindbrain embryo (15.5 days) +1581 ENCFF570FAF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR299NCJ/summary/ENCFF570FAF.w5 128 32 2.0 mean 1581 CHIP:H3K9me3:C57BL/6 hindbrain embryo (11.5 days) +1582 ENCFF349EPV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR302HOJ/summary/ENCFF349EPV.w5 128 32 2.0 mean 1582 CHIP:H3K27me3:C57BL/6 hindbrain embryo (12.5 days) +1583 ENCFF551UEX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR305GII/summary/ENCFF551UEX.w5 128 32 2.0 mean 1583 CHIP:H3K4me3:C57BL/6 lung embryo (15.5 days) +1584 ENCFF323FCP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR308GFM/summary/ENCFF323FCP.w5 128 32 2.0 mean 1584 CHIP:H3K4me1:C57BL/6 liver postnatal (0 days) +1585 ENCFF156SIF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR308TAV/summary/ENCFF156SIF.w5 128 32 2.0 mean 1585 CHIP:H3K27me3:C57BL/6 hindbrain postnatal (0 days) +1586 ENCFF492VCK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR311LZM/summary/ENCFF492VCK.w5 128 32 2.0 mean 1586 CHIP:H3K9me3:C57BL/6 lung embryo (14.5 days) +1587 ENCFF402XZO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR311TLE/summary/ENCFF402XZO.w5 128 32 2.0 mean 1587 CHIP:H3K9me3:C57BL/6 midbrain embryo (11.5 days) +1588 ENCFF776ZXU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR311VKI/summary/ENCFF776ZXU.w5 128 32 2.0 mean 1588 CHIP:H3K9me3:C57BL/6 intestine embryo (15.5 days) +1589 ENCFF107UHG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR311YPF/summary/ENCFF107UHG.w5 128 32 2.0 mean 1589 CHIP:H3K27ac:C57BL/6 forebrain embryo (13.5 days) +1590 ENCFF909MUJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR312BOK/summary/ENCFF909MUJ.w5 128 32 2.0 mean 1590 CHIP:H3K9ac:C57BL/6 midbrain embryo (12.5 days) +1591 ENCFF152HAY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR314FGC/summary/ENCFF152HAY.w5 128 32 2.0 mean 1591 CHIP:H3K4me2:C57BL/6 midbrain embryo (16.5 days) +1592 ENCFF356LUU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR315ZEU/summary/ENCFF356LUU.w5 128 32 2.0 mean 1592 CHIP:H3K4me3:C57BL/6 hindbrain embryo (13.5 days) +1593 ENCFF919YGD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR316AZB/summary/ENCFF919YGD.w5 128 32 2.0 mean 1593 CHIP:H3K9me3:C57BL/6 embryonic facial prominence embryo (12.5 days) +1594 ENCFF036PPT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR316CNR/summary/ENCFF036PPT.w5 128 32 2.0 mean 1594 CHIP:H3K27ac:C57BL/6 stomach embryo (14.5 days) +1595 ENCFF563HQA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR318QFY/summary/ENCFF563HQA.w5 128 32 2.0 mean 1595 CHIP:H3K4me3:C57BL/6 limb embryo (10.5 days) +1596 ENCFF627ZLA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR320CCJ/summary/ENCFF627ZLA.w5 128 32 2.0 mean 1596 CHIP:H3K4me3:C57BL/6 embryonic facial prominence embryo (11.5 days) +1597 ENCFF527FOD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR320EEW/summary/ENCFF527FOD.w5 128 32 2.0 mean 1597 CHIP:H3K27ac:C57BL/6 forebrain embryo (14.5 days) +1598 ENCFF354BAJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR320UJD/summary/ENCFF354BAJ.w5 128 32 2.0 mean 1598 CHIP:H3K4me3:C57BL/6 kidney embryo (15.5 days) +1599 ENCFF952PTF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR322XHD/summary/ENCFF952PTF.w5 128 32 2.0 mean 1599 CHIP:H3K4me2:C57BL/6 midbrain postnatal (0 days) +1600 ENCFF768DOK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR323NOC/summary/ENCFF768DOK.w5 128 32 2.0 mean 1600 CHIP:H3K4me2:C57BL/6 hindbrain embryo (11.5 days) +1601 ENCFF779TQD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR325JLI/summary/ENCFF779TQD.w5 128 32 2.0 mean 1601 CHIP:H3K9me3:C57BL/6 hindbrain embryo (13.5 days) +1602 ENCFF474PLN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR328WMV/summary/ENCFF474PLN.w5 128 32 2.0 mean 1602 CHIP:H3K36me3:C57BL/6 heart embryo (10.5 days) +1603 ENCFF665WCP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR332JYZ/summary/ENCFF665WCP.w5 128 32 2.0 mean 1603 CHIP:H3K27ac:C57BL/6 hindbrain postnatal (0 days) +1604 ENCFF641CTW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR332UCY/summary/ENCFF641CTW.w5 128 32 2.0 mean 1604 CHIP:H3K9ac:C57BL/6 limb embryo (15.5 days) +1605 ENCFF033IOU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR333QJO/summary/ENCFF033IOU.w5 128 32 2.0 mean 1605 CHIP:H3K9me3:C57BL/6 limb embryo (14.5 days) +1606 ENCFF877BSP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR333ZWB/summary/ENCFF877BSP.w5 128 32 2.0 mean 1606 CHIP:H3K4me2:C57BL/6 intestine postnatal (0 days) +1607 ENCFF576SVQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR335TVR/summary/ENCFF576SVQ.w5 128 32 2.0 mean 1607 CHIP:H3K4me3:C57BL/6 hindbrain embryo (15.5 days) +1608 ENCFF866OFV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR335WME/summary/ENCFF866OFV.w5 128 32 2.0 mean 1608 CHIP:H3K4me1:C57BL/6 stomach embryo (14.5 days) +1609 ENCFF035UHY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR337XUK/summary/ENCFF035UHY.w5 128 32 2.0 mean 1609 CHIP:H3K27me3:C57BL/6 liver embryo (14.5 days) +1610 ENCFF816ESX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR339LMJ/summary/ENCFF816ESX.w5 128 32 2.0 mean 1610 CHIP:H3K4me1:C57BL/6 heart embryo (15.5 days) +1611 ENCFF149AGA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR340ROY/summary/ENCFF149AGA.w5 128 32 2.0 mean 1611 CHIP:H3K27me3:C57BL/6 midbrain postnatal (0 days) +1612 ENCFF382IWW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR340VNK/summary/ENCFF382IWW.w5 128 32 2.0 mean 1612 CHIP:H3K4me2:C57BL/6 lung postnatal (0 days) +1613 ENCFF040LFN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR341XCL/summary/ENCFF040LFN.w5 128 32 2.0 mean 1613 CHIP:H3K9me3:C57BL/6 liver postnatal (0 days) +1614 ENCFF275WHD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR344BPJ/summary/ENCFF275WHD.w5 128 32 2.0 mean 1614 CHIP:H3K4me2:C57BL/6 liver embryo (14.5 days) +1615 ENCFF923TVC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR344HHI/summary/ENCFF923TVC.w5 128 32 2.0 mean 1615 CHIP:H3K27ac:C57BL/6 hindbrain embryo (13.5 days) +1616 ENCFF701NCZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR345DDI/summary/ENCFF701NCZ.w5 128 32 2.0 mean 1616 CHIP:H3K36me3:C57BL/6 forebrain embryo (12.5 days) +1617 ENCFF495VRT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR345HNA/summary/ENCFF495VRT.w5 128 32 2.0 mean 1617 CHIP:H3K9me3:C57BL/6 neural tube embryo (13.5 days) +1618 ENCFF770FZI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR345RKE/summary/ENCFF770FZI.w5 128 32 2.0 mean 1618 CHIP:H3K9ac:C57BL/6 heart embryo (14.5 days) +1619 ENCFF224LDB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR346FJG/summary/ENCFF224LDB.w5 128 32 2.0 mean 1619 CHIP:H3K27ac:C57BL/6 stomach postnatal (0 days) +1620 ENCFF323AGE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR347BFO/summary/ENCFF323AGE.w5 128 32 2.0 mean 1620 CHIP:H3K9ac:C57BL/6 midbrain embryo (15.5 days) +1621 ENCFF894YTN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR349JDH/summary/ENCFF894YTN.w5 128 32 2.0 mean 1621 CHIP:TCF12:DBA/2 MEL cell line +1622 ENCFF429OYS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR349NIS/summary/ENCFF429OYS.w5 128 32 2.0 mean 1622 CHIP:H3K4me1:C57BL/6 hindbrain embryo (13.5 days) +1623 ENCFF423EGY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR352AWJ/summary/ENCFF423EGY.w5 128 32 2.0 mean 1623 CHIP:H3K36me3:C57BL/6 forebrain embryo (16.5 days) +1624 ENCFF809PQF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR352NVU/summary/ENCFF809PQF.w5 128 32 2.0 mean 1624 CHIP:H3K9me3:C57BL/6 forebrain embryo (16.5 days) +1625 ENCFF820UTZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR356LBC/summary/ENCFF820UTZ.w5 128 32 2.0 mean 1625 CHIP:H3K9ac:C57BL/6 lung postnatal (0 days) +1626 ENCFF132TLS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR357JII/summary/ENCFF132TLS.w5 128 32 2.0 mean 1626 CHIP:H3K27ac:C57BL/6 kidney embryo (16.5 days) +1627 ENCFF129FZH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR357OED/summary/ENCFF129FZH.w5 128 32 2.0 mean 1627 CHIP:H3K27me3:C57BL/6 heart embryo (14.5 days) +1628 ENCFF981JRQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR358XYP/summary/ENCFF981JRQ.w5 128 32 2.0 mean 1628 CHIP:H3K9me3:C57BL/6 intestine embryo (16.5 days) +1629 ENCFF689PCR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR360ANE/summary/ENCFF689PCR.w5 128 32 2.0 mean 1629 CHIP:H3K27ac:C57BL/6 heart embryo (14.5 days) +1630 ENCFF363RRH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR362PBD/summary/ENCFF363RRH.w5 128 32 2.0 mean 1630 CHIP:H3K36me3:C57BL/6 kidney postnatal (0 days) +1631 ENCFF454YWR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR362VNF/summary/ENCFF454YWR.w5 128 32 2.0 mean 1631 CHIP:CTCF:129 E14TG2a.4 +1632 ENCFF919CSS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR365CUP/summary/ENCFF919CSS.w5 128 32 2.0 mean 1632 CHIP:H3K9me3:C57BL/6 hindbrain postnatal (0 days) +1633 ENCFF149KHB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR368RJD/summary/ENCFF149KHB.w5 128 32 2.0 mean 1633 CHIP:H3K4me3:C57BL/6 forebrain embryo (10.5 days) +1634 ENCFF841NIU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR369RBO/summary/ENCFF841NIU.w5 128 32 2.0 mean 1634 CHIP:H3K9ac:C57BL/6 forebrain postnatal (0 days) +1635 ENCFF558KHU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR370MSK/summary/ENCFF558KHU.w5 128 32 2.0 mean 1635 CHIP:H3K4me2:C57BL/6 neural tube embryo (12.5 days) +1636 ENCFF440SVM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR373LNE/summary/ENCFF440SVM.w5 128 32 2.0 mean 1636 CHIP:H3K9ac:C57BL/6 heart embryo (16.5 days) +1637 ENCFF099OBO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR373OCX/summary/ENCFF099OBO.w5 128 32 2.0 mean 1637 CHIP:H3K4me2:C57BL/6 heart postnatal (0 days) +1638 ENCFF421NWC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR373TMR/summary/ENCFF421NWC.w5 128 32 2.0 mean 1638 CHIP:H3K9ac:C57BL/6 forebrain embryo (13.5 days) +1639 ENCFF352EVI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR375GSG/summary/ENCFF352EVI.w5 128 32 2.0 mean 1639 CHIP:H3K27me3:C57BL/6 hindbrain embryo (11.5 days) +1640 ENCFF901MQW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR375RUA/summary/ENCFF901MQW.w5 128 32 2.0 mean 1640 CHIP:H3K27me3:C57BL/6 neural tube embryo (12.5 days) +1641 ENCFF062SWO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR377RKW/summary/ENCFF062SWO.w5 128 32 2.0 mean 1641 CHIP:H3K4me2:C57BL/6 heart embryo (15.5 days) +1642 ENCFF972QDT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR380BBL/summary/ENCFF972QDT.w5 128 32 2.0 mean 1642 CHIP:H3K27me3:C57BL/6 heart embryo (13.5 days) +1643 ENCFF033PTH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR382DRK/summary/ENCFF033PTH.w5 128 32 2.0 mean 1643 CHIP:H3K27ac:C57BL/6 embryonic facial prominence embryo (15.5 days) +1644 ENCFF534WMK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR387YSD/summary/ENCFF534WMK.w5 128 32 2.0 mean 1644 CHIP:H3K4me1:C57BL/6 lung embryo (16.5 days) +1645 ENCFF133XFD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR389EYR/summary/ENCFF133XFD.w5 128 32 2.0 mean 1645 CHIP:H3K27me3:C57BL/6 intestine postnatal (0 days) +1646 ENCFF143LAV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR391WSS/summary/ENCFF143LAV.w5 128 32 2.0 mean 1646 CHIP:H3K4me1:C57BL/6 midbrain postnatal (0 days) +1647 ENCFF619BQO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR392DGA/summary/ENCFF619BQO.w5 128 32 2.0 mean 1647 CHIP:POU5F1:129 E14TG2a.4 +1648 ENCFF691ULU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR397RHW/summary/ENCFF691ULU.w5 128 32 2.0 mean 1648 CHIP:CTCF:C57BL/6 liver embryo (14.5 days) +1649 ENCFF645JTI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR398TTY/summary/ENCFF645JTI.w5 128 32 2.0 mean 1649 CHIP:H3K4me2:C57BL/6 lung embryo (15.5 days) +1650 ENCFF324UGW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR399UVI/summary/ENCFF324UGW.w5 128 32 2.0 mean 1650 CHIP:H3K27me3:C57BL/6 kidney embryo (14.5 days) +1651 ENCFF855PPC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR400TGE/summary/ENCFF855PPC.w5 128 32 2.0 mean 1651 CHIP:H3K9ac:C57BL/6 forebrain embryo (11.5 days) +1652 ENCFF089IXS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR401GRX/summary/ENCFF089IXS.w5 128 32 2.0 mean 1652 CHIP:H3K27ac:C57BL/6 embryonic facial prominence embryo (11.5 days) +1653 ENCFF083ZPL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR402ZLE/summary/ENCFF083ZPL.w5 128 32 2.0 mean 1653 CHIP:H3K4me2:C57BL/6 forebrain embryo (15.5 days) +1654 ENCFF433RSJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR405TGI/summary/ENCFF433RSJ.w5 128 32 2.0 mean 1654 CHIP:H3K9me3:C57BL/6 kidney embryo (14.5 days) +1655 ENCFF671LRY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR406KDB/summary/ENCFF671LRY.w5 128 32 2.0 mean 1655 CHIP:H3K4me2:C57BL/6 heart embryo (12.5 days) +1656 ENCFF623HDU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR406VPQ/summary/ENCFF623HDU.w5 128 32 2.0 mean 1656 CHIP:H3K4me2:C57BL/6 embryonic facial prominence embryo (11.5 days) +1657 ENCFF525EWD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR410YIY/summary/ENCFF525EWD.w5 128 32 2.0 mean 1657 CHIP:H3K4me3:C57BL/6 intestine embryo (15.5 days) +1658 ENCFF104WUV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR412ODT/summary/ENCFF104WUV.w5 128 32 2.0 mean 1658 CHIP:H3K9ac:C57BL/6 intestine embryo (15.5 days) +1659 ENCFF290CLV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR415FLZ/summary/ENCFF290CLV.w5 128 32 2.0 mean 1659 CHIP:H3K4me2:C57BL/6 stomach embryo (15.5 days) +1660 ENCFF856ZXY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR416OYH/summary/ENCFF856ZXY.w5 128 32 2.0 mean 1660 CHIP:H3K4me3:C57BL/6 limb embryo (13.5 days) +1661 ENCFF056IYN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR417TXZ/summary/ENCFF056IYN.w5 128 32 2.0 mean 1661 CHIP:H3K4me1:C57BL/6 hindbrain embryo (14.5 days) +1662 ENCFF739QBQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR418SBY/summary/ENCFF739QBQ.w5 128 32 2.0 mean 1662 CHIP:CTCF:C57BL/6 lung postnatal (0 days) +1663 ENCFF654PSV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR419MSI/summary/ENCFF654PSV.w5 128 32 2.0 mean 1663 CHIP:H3K4me1:C57BL/6 liver embryo (11.5 days) +1664 ENCFF306YHS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR420MUV/summary/ENCFF306YHS.w5 128 32 2.0 mean 1664 CHIP:H3K27ac:C57BL/6 embryonic facial prominence embryo (13.5 days) +1665 ENCFF251XZW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR424END/summary/ENCFF251XZW.w5 128 32 2.0 mean 1665 CHIP:H3K27ac:C57BL/6 intestine embryo (14.5 days) +1666 ENCFF133NGW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR425FLT/summary/ENCFF133NGW.w5 128 32 2.0 mean 1666 CHIP:H3K36me3:C57BL/6 kidney embryo (14.5 days) +1667 ENCFF255RIU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR426EZM/summary/ENCFF255RIU.w5 128 32 2.0 mean 1667 CHIP:H3K4me1:C57BL/6 limb embryo (13.5 days) +1668 ENCFF638WLA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR427OZM/summary/ENCFF638WLA.w5 128 32 2.0 mean 1668 CHIP:H3K4me3:C57BL/6 neural tube embryo (11.5 days) +1669 ENCFF339HOE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR427ZJU/summary/ENCFF339HOE.w5 128 32 2.0 mean 1669 CHIP:H3K4me3:C57BL/6 midbrain postnatal (0 days) +1670 ENCFF637BYB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR427ZQB/summary/ENCFF637BYB.w5 128 32 2.0 mean 1670 CHIP:H3K9me3:C57BL/6 hindbrain embryo (16.5 days) +1671 ENCFF616CNP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR428GHF/summary/ENCFF616CNP.w5 128 32 2.0 mean 1671 CHIP:H3K27ac:C57BL/6 midbrain embryo (15.5 days) +1672 ENCFF826KEG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR428OEK/summary/ENCFF826KEG.w5 128 32 2.0 mean 1672 CHIP:H3K27ac:C57BL/6 forebrain embryo (16.5 days) +1673 ENCFF163DQS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR430JWT/summary/ENCFF163DQS.w5 128 32 2.0 mean 1673 CHIP:H3K9ac:C57BL/6 lung embryo (16.5 days) +1674 ENCFF118SNE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR433ESG/summary/ENCFF118SNE.w5 128 32 2.0 mean 1674 CHIP:H3K4me3:C57BL/6 liver embryo (14.5 days) +1675 ENCFF436MUY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR436FYE/summary/ENCFF436MUY.w5 128 32 2.0 mean 1675 CHIP:H3K4me1:C57BL/6 kidney embryo (15.5 days) +1676 ENCFF044FTG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR437NPG/summary/ENCFF044FTG.w5 128 32 2.0 mean 1676 CHIP:H3K27me3:C57BL/6 heart embryo (15.5 days) +1677 ENCFF393XPO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR437SFX/summary/ENCFF393XPO.w5 128 32 2.0 mean 1677 CHIP:H3K36me3:C57BL/6 forebrain embryo (15.5 days) +1678 ENCFF131MXX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR442RYY/summary/ENCFF131MXX.w5 128 32 2.0 mean 1678 CHIP:H3K4me1:C57BL/6 heart embryo (12.5 days) +1679 ENCFF362GRX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR445UYH/summary/ENCFF362GRX.w5 128 32 2.0 mean 1679 CHIP:H3K36me3:C57BL/6 neural tube embryo (11.5 days) +1680 ENCFF350KKE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR447BVY/summary/ENCFF350KKE.w5 128 32 2.0 mean 1680 CHIP:H3K36me3:C57BL/6 embryonic facial prominence embryo (13.5 days) +1681 ENCFF053JUA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR447DOF/summary/ENCFF053JUA.w5 128 32 2.0 mean 1681 CHIP:H3K4me3:C57BL/6 liver embryo (11.5 days) +1682 ENCFF813VAT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR448TTC/summary/ENCFF813VAT.w5 128 32 2.0 mean 1682 CHIP:H3K4me1:C57BL/6 neural tube embryo (11.5 days) +1683 ENCFF833YTL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR449EUZ/summary/ENCFF833YTL.w5 128 32 2.0 mean 1683 CHIP:H3K4me1:C57BL/6 midbrain embryo (15.5 days) +1684 ENCFF554FAE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR450ITF/summary/ENCFF554FAE.w5 128 32 2.0 mean 1684 CHIP:H3K4me1:C57BL/6 midbrain embryo (11.5 days) +1685 ENCFF665UTM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR450KVW/summary/ENCFF665UTM.w5 128 32 2.0 mean 1685 CHIP:EP300:C57BL/6 stomach postnatal (0 days) +1686 ENCFF173XOV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR452WYC/summary/ENCFF173XOV.w5 128 32 2.0 mean 1686 CHIP:H3K27ac:C57BL/6 lung embryo (14.5 days) +1687 ENCFF172OCI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR455REA/summary/ENCFF172OCI.w5 128 32 2.0 mean 1687 CHIP:H3K9me3:C57BL/6 heart embryo (10.5 days) +1688 ENCFF952ZFO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR455UTX/summary/ENCFF952ZFO.w5 128 32 2.0 mean 1688 CHIP:H3K36me3:C57BL/6 kidney embryo (15.5 days) +1689 ENCFF344FSI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR457HDY/summary/ENCFF344FSI.w5 128 32 2.0 mean 1689 CHIP:H3K27me3:C57BL/6 embryonic facial prominence embryo (14.5 days) +1690 ENCFF362OAA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR458FBL/summary/ENCFF362OAA.w5 128 32 2.0 mean 1690 CHIP:H3K4me2:C57BL/6 liver embryo (16.5 days) +1691 ENCFF562BME /home/drk/tillage/datasets/mouse/chip/encode/ENCSR458PAO/summary/ENCFF562BME.w5 128 32 2.0 mean 1691 CHIP:H3K36me3:C57BL/6 hindbrain postnatal (0 days) +1692 ENCFF534ANR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR462BZP/summary/ENCFF534ANR.w5 128 32 2.0 mean 1692 CHIP:H3K9ac:C57BL/6 limb embryo (13.5 days) +1693 ENCFF181ZVG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR462KTT/summary/ENCFF181ZVG.w5 128 32 2.0 mean 1693 CHIP:H3K4me2:C57BL/6 forebrain embryo (16.5 days) +1694 ENCFF207EPW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR463GJL/summary/ENCFF207EPW.w5 128 32 2.0 mean 1694 CHIP:H3K9me3:C57BL/6 heart embryo (11.5 days) +1695 ENCFF751FCH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR464MQU/summary/ENCFF751FCH.w5 128 32 2.0 mean 1695 CHIP:H3K4me3:C57BL/6 intestine embryo (14.5 days) +1696 ENCFF695KNJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR465PLB/summary/ENCFF695KNJ.w5 128 32 2.0 mean 1696 CHIP:H3K4me1:C57BL/6 forebrain postnatal (0 days) +1697 ENCFF025FNF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR465TIZ/summary/ENCFF025FNF.w5 128 32 2.0 mean 1697 CHIP:H3K27me3:C57BL/6 midbrain embryo (16.5 days) +1698 ENCFF973ZKZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR466ZQC/summary/ENCFF973ZKZ.w5 128 32 2.0 mean 1698 CHIP:H3K9me3:C57BL/6 neural tube embryo (11.5 days) +1699 ENCFF686TFW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR467UGM/summary/ENCFF686TFW.w5 128 32 2.0 mean 1699 CHIP:H3K36me3:C57BL/6 heart embryo (16.5 days) +1700 ENCFF487TJN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR471SJG/summary/ENCFF487TJN.w5 128 32 2.0 mean 1700 CHIP:H3K4me3:C57BL/6 liver embryo (12.5 days) +1701 ENCFF669USU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR472YGQ/summary/ENCFF669USU.w5 128 32 2.0 mean 1701 CHIP:H3K4me3:C57BL/6 hindbrain postnatal (0 days) +1702 ENCFF290NHP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR479LFP/summary/ENCFF290NHP.w5 128 32 2.0 mean 1702 CHIP:H3K27ac:C57BL/6 liver embryo (15.5 days) +1703 ENCFF071HGW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR481SGM/summary/ENCFF071HGW.w5 128 32 2.0 mean 1703 CHIP:H3K27ac:C57BL/6 embryonic facial prominence embryo (14.5 days) +1704 ENCFF419ZKE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR483DEV/summary/ENCFF419ZKE.w5 128 32 2.0 mean 1704 CHIP:H3K9ac:C57BL/6 stomach embryo (15.5 days) +1705 ENCFF085HHF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR483KOD/summary/ENCFF085HHF.w5 128 32 2.0 mean 1705 CHIP:H3K36me3:C57BL/6 intestine postnatal (0 days) +1706 ENCFF766FZH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR485GTY/summary/ENCFF766FZH.w5 128 32 2.0 mean 1706 CHIP:H3K4me2:C57BL/6 intestine embryo (14.5 days) +1707 ENCFF724CMA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR486MHP/summary/ENCFF724CMA.w5 128 32 2.0 mean 1707 CHIP:H3K4me3:C57BL/6 midbrain embryo (15.5 days) +1708 ENCFF544BIS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR487OLC/summary/ENCFF544BIS.w5 128 32 2.0 mean 1708 CHIP:H3K4me1:C57BL/6 liver embryo (16.5 days) +1709 ENCFF565NEA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR487RAU/summary/ENCFF565NEA.w5 128 32 2.0 mean 1709 CHIP:H3K36me3:C57BL/6 midbrain embryo (15.5 days) +1710 ENCFF064NXP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR488KVB/summary/ENCFF064NXP.w5 128 32 2.0 mean 1710 CHIP:H3K4me2:C57BL/6 limb embryo (12.5 days) +1711 ENCFF577SJR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR488OCA/summary/ENCFF577SJR.w5 128 32 2.0 mean 1711 CHIP:H3K4me1:C57BL/6 heart postnatal (0 days) +1712 ENCFF338BLF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR489HYX/summary/ENCFF338BLF.w5 128 32 2.0 mean 1712 CHIP:H3K4me2:C57BL/6 neural tube embryo (11.5 days) +1713 ENCFF278NWO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR491NUM/summary/ENCFF278NWO.w5 128 32 2.0 mean 1713 CHIP:CTCF:C57BL/6 heart postnatal (0 days) +1714 ENCFF905MWT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR496TBX/summary/ENCFF905MWT.w5 128 32 2.0 mean 1714 CHIP:H3K4me1:C57BL/6 forebrain embryo (13.5 days) +1715 ENCFF517QXW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR498EVD/summary/ENCFF517QXW.w5 128 32 2.0 mean 1715 CHIP:H3K9me3:C57BL/6 kidney postnatal (0 days) +1716 ENCFF209XEZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR499NUH/summary/ENCFF209XEZ.w5 128 32 2.0 mean 1716 CHIP:H3K9me3:C57BL/6 kidney embryo (15.5 days) +1717 ENCFF054NVM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR501GBJ/summary/ENCFF054NVM.w5 128 32 2.0 mean 1717 CHIP:H3K4me3:C57BL/6 heart embryo (13.5 days) +1718 ENCFF794MAE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR502WUI/summary/ENCFF794MAE.w5 128 32 2.0 mean 1718 CHIP:H3K9ac:C57BL/6 midbrain embryo (11.5 days) +1719 ENCFF073JCW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR508HYL/summary/ENCFF073JCW.w5 128 32 2.0 mean 1719 CHIP:H3K36me3:C57BL/6 hindbrain embryo (12.5 days) +1720 ENCFF397XOU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR510CGB/summary/ENCFF397XOU.w5 128 32 2.0 mean 1720 CHIP:H3K36me3:C57BL/6 liver embryo (15.5 days) +1721 ENCFF258NLM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR511LWL/summary/ENCFF258NLM.w5 128 32 2.0 mean 1721 CHIP:H3K9ac:C57BL/6 neural tube embryo (14.5 days) +1722 ENCFF832GKC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR511WPK/summary/ENCFF832GKC.w5 128 32 2.0 mean 1722 CHIP:H3K4me1:C57BL/6 embryonic facial prominence embryo (11.5 days) +1723 ENCFF893IAL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR515XWH/summary/ENCFF893IAL.w5 128 32 2.0 mean 1723 CHIP:H3K27me3:C57BL/6 intestine embryo (16.5 days) +1724 ENCFF307IYH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR516KLO/summary/ENCFF307IYH.w5 128 32 2.0 mean 1724 CHIP:H3K36me3:C57BL/6 stomach postnatal (0 days) +1725 ENCFF235MDM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR516TYD/summary/ENCFF235MDM.w5 128 32 2.0 mean 1725 CHIP:H3K4me2:C57BL/6 kidney postnatal (0 days) +1726 ENCFF087WAM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR517UZA/summary/ENCFF087WAM.w5 128 32 2.0 mean 1726 CHIP:H3K4me2:C57BL/6 neural tube embryo (15.5 days) +1727 ENCFF042PHG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR519DNE/summary/ENCFF042PHG.w5 128 32 2.0 mean 1727 CHIP:H3K9ac:C57BL/6 heart postnatal (0 days) +1728 ENCFF180VGZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR522LXN/summary/ENCFF180VGZ.w5 128 32 2.0 mean 1728 CHIP:H3K4me3:C57BL/6 stomach embryo (15.5 days) +1729 ENCFF970OZN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR523IIH/summary/ENCFF970OZN.w5 128 32 2.0 mean 1729 CHIP:H3K4me1:C57BL/6 lung postnatal (0 days) +1730 ENCFF777NSG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR525BTK/summary/ENCFF777NSG.w5 128 32 2.0 mean 1730 CHIP:H3K4me2:C57BL/6 midbrain embryo (15.5 days) +1731 ENCFF505IIX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR526JRI/summary/ENCFF505IIX.w5 128 32 2.0 mean 1731 CHIP:H3K9me3:C57BL/6 embryonic facial prominence embryo (11.5 days) +1732 ENCFF583XLF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR527DME/summary/ENCFF583XLF.w5 128 32 2.0 mean 1732 CHIP:EP300:C57BL/6 lung postnatal (0 days) +1733 ENCFF178JLS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR527EUE/summary/ENCFF178JLS.w5 128 32 2.0 mean 1733 CHIP:H3K4me3:C57BL/6 forebrain embryo (12.5 days) +1734 ENCFF606BGM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR529ERN/summary/ENCFF606BGM.w5 128 32 2.0 mean 1734 CHIP:H3K4me1:C57BL/6 limb embryo (14.5 days) +1735 ENCFF422NJA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR531RZS/summary/ENCFF422NJA.w5 128 32 2.0 mean 1735 CHIP:H3K27ac:C57BL/6 neural tube embryo (11.5 days) +1736 ENCFF159AEV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR534HMF/summary/ENCFF159AEV.w5 128 32 2.0 mean 1736 CHIP:H3K4me2:C57BL/6 heart embryo (14.5 days) +1737 ENCFF208SBA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR535NVF/summary/ENCFF208SBA.w5 128 32 2.0 mean 1737 CHIP:H3K36me3:C57BL/6 midbrain embryo (11.5 days) +1738 ENCFF376RQB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR536ILV/summary/ENCFF376RQB.w5 128 32 2.0 mean 1738 CHIP:H3K4me3:C57BL/6 kidney postnatal (0 days) +1739 ENCFF323VNT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR537AKT/summary/ENCFF323VNT.w5 128 32 2.0 mean 1739 CHIP:H3K4me2:C57BL/6 hindbrain embryo (12.5 days) +1740 ENCFF644DVO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR538DPG/summary/ENCFF644DVO.w5 128 32 2.0 mean 1740 CHIP:H3K36me3:C57BL/6 embryonic facial prominence embryo (10.5 days) +1741 ENCFF552KFS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR538SRO/summary/ENCFF552KFS.w5 128 32 2.0 mean 1741 CHIP:H3K4me3:C57BL/6 neural tube embryo (12.5 days) +1742 ENCFF485WCD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR545BRW/summary/ENCFF485WCD.w5 128 32 2.0 mean 1742 CHIP:H3K27me3:C57BL/6 midbrain embryo (11.5 days) +1743 ENCFF069OMF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR546ANT/summary/ENCFF069OMF.w5 128 32 2.0 mean 1743 CHIP:H3K27ac:C57BL/6 stomach embryo (16.5 days) +1744 ENCFF358FNS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR547PLI/summary/ENCFF358FNS.w5 128 32 2.0 mean 1744 CHIP:H3K9ac:C57BL/6 neural tube embryo (11.5 days) +1745 ENCFF956BOI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR548BCO/summary/ENCFF956BOI.w5 128 32 2.0 mean 1745 CHIP:H3K4me1:C57BL/6 limb embryo (11.5 days) +1746 ENCFF179UEK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR548BKP/summary/ENCFF179UEK.w5 128 32 2.0 mean 1746 CHIP:H3K4me1:C57BL/6 stomach embryo (15.5 days) +1747 ENCFF987UOT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR549RVJ/summary/ENCFF987UOT.w5 128 32 2.0 mean 1747 CHIP:H3K9me3:C57BL/6 neural tube embryo (15.5 days) +1748 ENCFF914LRA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR550QED/summary/ENCFF914LRA.w5 128 32 2.0 mean 1748 CHIP:H3K27me3:C57BL/6 liver embryo (13.5 days) +1749 ENCFF447LGJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR553IWV/summary/ENCFF447LGJ.w5 128 32 2.0 mean 1749 CHIP:H3K27ac:C57BL/6 midbrain embryo (16.5 days) +1750 ENCFF682ZKK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR554TSO/summary/ENCFF682ZKK.w5 128 32 2.0 mean 1750 CHIP:H3K4me3:C57BL/6 midbrain embryo (12.5 days) +1751 ENCFF591NXE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR556DLJ/summary/ENCFF591NXE.w5 128 32 2.0 mean 1751 CHIP:H3K9me3:C57BL/6 stomach postnatal (0 days) +1752 ENCFF586OQX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR556ZUY/summary/ENCFF586OQX.w5 128 32 2.0 mean 1752 CHIP:H3K4me1:C57BL/6 forebrain embryo (14.5 days) +1753 ENCFF797OAF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR557SVH/summary/ENCFF797OAF.w5 128 32 2.0 mean 1753 CHIP:H3K9me3:C57BL/6 heart embryo (12.5 days) +1754 ENCFF450RTN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR558NWQ/summary/ENCFF450RTN.w5 128 32 2.0 mean 1754 CHIP:H3K36me3:C57BL/6 forebrain embryo (10.5 days) +1755 ENCFF309BMY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR560CIG/summary/ENCFF309BMY.w5 128 32 2.0 mean 1755 CHIP:H3K36me3:C57BL/6 heart embryo (15.5 days) +1756 ENCFF460ZYC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR564JKR/summary/ENCFF460ZYC.w5 128 32 2.0 mean 1756 CHIP:H3K27me3:C57BL/6 kidney postnatal (0 days) +1757 ENCFF848GOF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR564XSR/summary/ENCFF848GOF.w5 128 32 2.0 mean 1757 CHIP:H3K27me3:C57BL/6 forebrain embryo (15.5 days) +1758 ENCFF702EWM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR569DBO/summary/ENCFF702EWM.w5 128 32 2.0 mean 1758 CHIP:H3K36me3:C57BL/6 liver embryo (16.5 days) +1759 ENCFF244GAG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR569UCG/summary/ENCFF244GAG.w5 128 32 2.0 mean 1759 CHIP:H3K9ac:C57BL/6 kidney embryo (14.5 days) +1760 ENCFF520CMB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR570HJI/summary/ENCFF520CMB.w5 128 32 2.0 mean 1760 CHIP:H3K27me3:C57BL/6 liver embryo (15.5 days) +1761 ENCFF197IGU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR571HOT/summary/ENCFF197IGU.w5 128 32 2.0 mean 1761 CHIP:H3K9ac:C57BL/6 neural tube embryo (15.5 days) +1762 ENCFF390PNF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR571WQI/summary/ENCFF390PNF.w5 128 32 2.0 mean 1762 CHIP:H3K9me3:C57BL/6 midbrain embryo (16.5 days) +1763 ENCFF029WVD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR572KYR/summary/ENCFF029WVD.w5 128 32 2.0 mean 1763 CHIP:H3K4me3:C57BL/6 intestine embryo (16.5 days) +1764 ENCFF021RTZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR574VME/summary/ENCFF021RTZ.w5 128 32 2.0 mean 1764 CHIP:H3K27ac:C57BL/6 heart embryo (15.5 days) +1765 ENCFF017FCI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR576XBN/summary/ENCFF017FCI.w5 128 32 2.0 mean 1765 CHIP:H3K9ac:C57BL/6 hindbrain embryo (12.5 days) +1766 ENCFF960DLF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR577SDJ/summary/ENCFF960DLF.w5 128 32 2.0 mean 1766 CHIP:H3K4me3:C57BL/6 liver embryo (15.5 days) +1767 ENCFF817VNI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR578RLI/summary/ENCFF817VNI.w5 128 32 2.0 mean 1767 CHIP:H3K4me2:C57BL/6 liver postnatal (0 days) +1768 ENCFF161KBG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR579RZO/summary/ENCFF161KBG.w5 128 32 2.0 mean 1768 CHIP:H3K4me2:C57BL/6 neural tube embryo (14.5 days) +1769 ENCFF828TZR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR579UVB/summary/ENCFF828TZR.w5 128 32 2.0 mean 1769 CHIP:H3K9me3:C57BL/6 lung embryo (16.5 days) +1770 ENCFF009QET /home/drk/tillage/datasets/mouse/chip/encode/ENCSR580MEU/summary/ENCFF009QET.w5 128 32 2.0 mean 1770 CHIP:H3K27me3:C57BL/6 neural tube embryo (13.5 days) +1771 ENCFF197CLN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR581EJK/summary/ENCFF197CLN.w5 128 32 2.0 mean 1771 CHIP:H3K4me3:C57BL/6 midbrain embryo (10.5 days) +1772 ENCFF450GMP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR581FAT/summary/ENCFF450GMP.w5 128 32 2.0 mean 1772 CHIP:H3K36me3:C57BL/6 stomach embryo (14.5 days) +1773 ENCFF772NBP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR582IBX/summary/ENCFF772NBP.w5 128 32 2.0 mean 1773 CHIP:H3K36me3:C57BL/6 embryonic facial prominence embryo (12.5 days) +1774 ENCFF222TEU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR582SPN/summary/ENCFF222TEU.w5 128 32 2.0 mean 1774 CHIP:H3K27ac:C57BL/6 heart embryo (10.5 days) +1775 ENCFF564SDZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR592GQI/summary/ENCFF564SDZ.w5 128 32 2.0 mean 1775 CHIP:H3K4me3:C57BL/6 heart embryo (11.5 days) +1776 ENCFF782RAO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR594JGI/summary/ENCFF782RAO.w5 128 32 2.0 mean 1776 CHIP:H3K27ac:C57BL/6 hindbrain embryo (10.5 days) +1777 ENCFF803SVJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR599GVS/summary/ENCFF803SVJ.w5 128 32 2.0 mean 1777 CHIP:H3K27ac:C57BL/6 intestine embryo (15.5 days) +1778 ENCFF966UNT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR599PKR/summary/ENCFF966UNT.w5 128 32 2.0 mean 1778 CHIP:H3K36me3:C57BL/6 stomach embryo (15.5 days) +1779 ENCFF296YDU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR604AMS/summary/ENCFF296YDU.w5 128 32 2.0 mean 1779 CHIP:H3K4me2:C57BL/6 intestine embryo (15.5 days) +1780 ENCFF965EJR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR604DCI/summary/ENCFF965EJR.w5 128 32 2.0 mean 1780 CHIP:H3K36me3:C57BL/6 embryonic facial prominence embryo (14.5 days) +1781 ENCFF738IHC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR604XDL/summary/ENCFF738IHC.w5 128 32 2.0 mean 1781 CHIP:MAFK:129 ES-E14 +1782 ENCFF464IYE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR606AJV/summary/ENCFF464IYE.w5 128 32 2.0 mean 1782 CHIP:H3K36me3:C57BL/6 embryonic facial prominence embryo (15.5 days) +1783 ENCFF705MBY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR607HIQ/summary/ENCFF705MBY.w5 128 32 2.0 mean 1783 CHIP:H3K9ac:C57BL/6 liver embryo (12.5 days) +1784 ENCFF089CJB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR607QZE/summary/ENCFF089CJB.w5 128 32 2.0 mean 1784 CHIP:H3K27me3:C57BL/6 kidney embryo (16.5 days) +1785 ENCFF894YHQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR608QBO/summary/ENCFF894YHQ.w5 128 32 2.0 mean 1785 CHIP:H3K4me1:C57BL/6 hindbrain embryo (10.5 days) +1786 ENCFF588AKC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR616TJM/summary/ENCFF588AKC.w5 128 32 2.0 mean 1786 CHIP:H3K27ac:C57BL/6 liver postnatal (0 days) +1787 ENCFF925YTU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR617VBE/summary/ENCFF925YTU.w5 128 32 2.0 mean 1787 CHIP:H3K4me1:C57BL/6 hindbrain postnatal (0 days) +1788 ENCFF750BCM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR629AFL/summary/ENCFF750BCM.w5 128 32 2.0 mean 1788 CHIP:H3K9ac:C57BL/6 limb embryo (12.5 days) +1789 ENCFF824UJK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR630AOU/summary/ENCFF824UJK.w5 128 32 2.0 mean 1789 CHIP:H3K9me3:C57BL/6 stomach embryo (16.5 days) +1790 ENCFF477XJO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR631KAJ/summary/ENCFF477XJO.w5 128 32 2.0 mean 1790 CHIP:H3K36me3:C57BL/6 heart embryo (11.5 days) +1791 ENCFF977AQW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR631QAE/summary/ENCFF977AQW.w5 128 32 2.0 mean 1791 CHIP:H3K4me2:C57BL/6 limb embryo (14.5 days) +1792 ENCFF137LNV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR634GFJ/summary/ENCFF137LNV.w5 128 32 2.0 mean 1792 CHIP:H3K9me3:C57BL/6 forebrain embryo (12.5 days) +1793 ENCFF644PLR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR637CCT/summary/ENCFF644PLR.w5 128 32 2.0 mean 1793 CHIP:H3K4me3:C57BL/6 midbrain embryo (16.5 days) +1794 ENCFF829GXB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR639DND/summary/ENCFF829GXB.w5 128 32 2.0 mean 1794 CHIP:H3K27ac:C57BL/6 intestine embryo (16.5 days) +1795 ENCFF769VJF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR639IQR/summary/ENCFF769VJF.w5 128 32 2.0 mean 1795 CHIP:H3K36me3:C57BL/6 limb embryo (13.5 days) +1796 ENCFF758CLJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR639KSW/summary/ENCFF758CLJ.w5 128 32 2.0 mean 1796 CHIP:H3K9ac:C57BL/6 hindbrain embryo (15.5 days) +1797 ENCFF152GZF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR641EME/summary/ENCFF152GZF.w5 128 32 2.0 mean 1797 CHIP:H3K36me3:C57BL/6 heart embryo (14.5 days) +1798 ENCFF512TCI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR642VYW/summary/ENCFF512TCI.w5 128 32 2.0 mean 1798 CHIP:H3K27ac:C57BL/6 intestine postnatal (0 days) +1799 ENCFF361SUJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR642ZLN/summary/ENCFF361SUJ.w5 128 32 2.0 mean 1799 CHIP:H3K27me3:C57BL/6 liver embryo (12.5 days) +1800 ENCFF140IVD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR645ETR/summary/ENCFF140IVD.w5 128 32 2.0 mean 1800 CHIP:H3K4me1:C57BL/6 embryonic facial prominence embryo (12.5 days) +1801 ENCFF109NPC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR647OTD/summary/ENCFF109NPC.w5 128 32 2.0 mean 1801 CHIP:H3K4me3:C57BL/6 heart embryo (15.5 days) +1802 ENCFF019ABU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR650UAC/summary/ENCFF019ABU.w5 128 32 2.0 mean 1802 CHIP:H3K4me2:C57BL/6 heart embryo (13.5 days) +1803 ENCFF615IVU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR653AVN/summary/ENCFF615IVU.w5 128 32 2.0 mean 1803 CHIP:H3K4me3:C57BL/6 liver postnatal (0 days) +1804 ENCFF306YUK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR654VMK/summary/ENCFF306YUK.w5 128 32 2.0 mean 1804 CHIP:H3K4me3:C57BL/6 limb embryo (11.5 days) +1805 ENCFF555EBK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR656AMS/summary/ENCFF555EBK.w5 128 32 2.0 mean 1805 CHIP:H3K36me3:C57BL/6 liver postnatal (0 days) +1806 ENCFF935NKI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR658BBG/summary/ENCFF935NKI.w5 128 32 2.0 mean 1806 CHIP:H3K27me3:C57BL/6 forebrain embryo (16.5 days) +1807 ENCFF774ZAY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR658TDS/summary/ENCFF774ZAY.w5 128 32 2.0 mean 1807 CHIP:H3K4me2:C57BL/6 kidney embryo (14.5 days) +1808 ENCFF673JMS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR663VWL/summary/ENCFF673JMS.w5 128 32 2.0 mean 1808 CHIP:H3K4me1:C57BL/6 heart embryo (13.5 days) +1809 ENCFF718RMZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR668BBX/summary/ENCFF718RMZ.w5 128 32 2.0 mean 1809 CHIP:H3K9me3:C57BL/6 forebrain embryo (15.5 days) +1810 ENCFF696ITD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR669AQL/summary/ENCFF696ITD.w5 128 32 2.0 mean 1810 CHIP:H3K4me3:C57BL/6 kidney embryo (14.5 days) +1811 ENCFF426WOD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR670YXP/summary/ENCFF426WOD.w5 128 32 2.0 mean 1811 CHIP:H3K36me3:C57BL/6 liver embryo (14.5 days) +1812 ENCFF416UPA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR671NSS/summary/ENCFF416UPA.w5 128 32 2.0 mean 1812 CHIP:H3K27ac:C57BL/6 midbrain embryo (13.5 days) +1813 ENCFF363IUI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR672UQX/summary/ENCFF363IUI.w5 128 32 2.0 mean 1813 CHIP:H3K9me3:C57BL/6 intestine postnatal (0 days) +1814 ENCFF961KLD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR672ZXY/summary/ENCFF961KLD.w5 128 32 2.0 mean 1814 CHIP:H3K27ac:C57BL/6 midbrain postnatal (0 days) +1815 ENCFF317OTS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR674PZU/summary/ENCFF317OTS.w5 128 32 2.0 mean 1815 CHIP:H3K4me1:C57BL/6 kidney postnatal (0 days) +1816 ENCFF804EYG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR675HDX/summary/ENCFF804EYG.w5 128 32 2.0 mean 1816 CHIP:H3K27ac:C57BL/6 heart postnatal (0 days) +1817 ENCFF500SSQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR677HXC/summary/ENCFF500SSQ.w5 128 32 2.0 mean 1817 CHIP:CTCF:C57BL/6 forebrain postnatal (0 days) +1818 ENCFF176KNA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR677SIH/summary/ENCFF176KNA.w5 128 32 2.0 mean 1818 CHIP:CTCF:C57BL/6 lung embryo (14.5 days) +1819 ENCFF298SER /home/drk/tillage/datasets/mouse/chip/encode/ENCSR678FIT/summary/ENCFF298SER.w5 128 32 2.0 mean 1819 CHIP:H3K4me1:C57BL/6 midbrain embryo (16.5 days) +1820 ENCFF309WXH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR684UWM/summary/ENCFF309WXH.w5 128 32 2.0 mean 1820 CHIP:H3K4me3:C57BL/6 stomach embryo (16.5 days) +1821 ENCFF331OQE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR688ZOR/summary/ENCFF331OQE.w5 128 32 2.0 mean 1821 CHIP:H3K4me3:C57BL/6 heart embryo (12.5 days) +1822 ENCFF463QJN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR689NXE/summary/ENCFF463QJN.w5 128 32 2.0 mean 1822 CHIP:H3K9me3:C57BL/6 hindbrain embryo (14.5 days) +1823 ENCFF440SCC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR691NQH/summary/ENCFF440SCC.w5 128 32 2.0 mean 1823 CHIP:H3K27ac:C57BL/6 forebrain embryo (15.5 days) +1824 ENCFF690UIX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR693UWX/summary/ENCFF690UIX.w5 128 32 2.0 mean 1824 CHIP:H3K4me2:C57BL/6 liver embryo (11.5 days) +1825 ENCFF124AFN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR695FPP/summary/ENCFF124AFN.w5 128 32 2.0 mean 1825 CHIP:H3K4me1:C57BL/6 hindbrain embryo (11.5 days) +1826 ENCFF814OZR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR698WCJ/summary/ENCFF814OZR.w5 128 32 2.0 mean 1826 CHIP:H3K9me3:C57BL/6 intestine embryo (14.5 days) +1827 ENCFF870SQY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR699XHY/summary/ENCFF870SQY.w5 128 32 2.0 mean 1827 CHIP:H3K27ac:C57BL/6 heart embryo (13.5 days) +1828 ENCFF422AUK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR701GKO/summary/ENCFF422AUK.w5 128 32 2.0 mean 1828 CHIP:H3K27me3:C57BL/6 embryonic facial prominence embryo (11.5 days) +1829 ENCFF997AJH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR702JYV/summary/ENCFF997AJH.w5 128 32 2.0 mean 1829 CHIP:H3K36me3:C57BL/6 midbrain embryo (14.5 days) +1830 ENCFF672EXE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR703TBR/summary/ENCFF672EXE.w5 128 32 2.0 mean 1830 CHIP:H3K9me3:C57BL/6 hindbrain embryo (10.5 days) +1831 ENCFF293PAY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR704IWS/summary/ENCFF293PAY.w5 128 32 2.0 mean 1831 CHIP:H3K4me3:C57BL/6 neural tube embryo (13.5 days) +1832 ENCFF377WET /home/drk/tillage/datasets/mouse/chip/encode/ENCSR705HGT/summary/ENCFF377WET.w5 128 32 2.0 mean 1832 CHIP:USF1:DBA/2 MEL cell line +1833 ENCFF769YBW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR706PSQ/summary/ENCFF769YBW.w5 128 32 2.0 mean 1833 CHIP:H3K4me2:C57BL/6 midbrain embryo (13.5 days) +1834 ENCFF933OKD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR706SZI/summary/ENCFF933OKD.w5 128 32 2.0 mean 1834 CHIP:H3K9me3:C57BL/6 embryonic facial prominence embryo (14.5 days) +1835 ENCFF399YKQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR707DZS/summary/ENCFF399YKQ.w5 128 32 2.0 mean 1835 CHIP:H3K4me2:C57BL/6 midbrain embryo (12.5 days) +1836 ENCFF779RNO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR709CLU/summary/ENCFF779RNO.w5 128 32 2.0 mean 1836 CHIP:H3K27me3:C57BL/6 limb embryo (13.5 days) +1837 ENCFF297RMH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR711SVB/summary/ENCFF297RMH.w5 128 32 2.0 mean 1837 CHIP:H3K27ac:C57BL/6 kidney embryo (15.5 days) +1838 ENCFF391DVK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR717XCU/summary/ENCFF391DVK.w5 128 32 2.0 mean 1838 CHIP:H3K9ac:C57BL/6 forebrain embryo (15.5 days) +1839 ENCFF810BQP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR718CAJ/summary/ENCFF810BQP.w5 128 32 2.0 mean 1839 CHIP:H3K9ac:C57BL/6 hindbrain embryo (16.5 days) +1840 ENCFF638WTR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR721MSV/summary/ENCFF638WTR.w5 128 32 2.0 mean 1840 CHIP:H3K9ac:C57BL/6 hindbrain postnatal (0 days) +1841 ENCFF863DGY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR731KRE/summary/ENCFF863DGY.w5 128 32 2.0 mean 1841 CHIP:H3K4me3:C57BL/6 hindbrain embryo (10.5 days) +1842 ENCFF581EFO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR731OMP/summary/ENCFF581EFO.w5 128 32 2.0 mean 1842 CHIP:H3K4me2:C57BL/6 liver embryo (13.5 days) +1843 ENCFF923XEA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR734IEL/summary/ENCFF923XEA.w5 128 32 2.0 mean 1843 CHIP:H3K9ac:C57BL/6 hindbrain embryo (11.5 days) +1844 ENCFF063ZLI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR735VEJ/summary/ENCFF063ZLI.w5 128 32 2.0 mean 1844 CHIP:H3K27me3:C57BL/6 forebrain embryo (10.5 days) +1845 ENCFF760VJL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR736GVO/summary/ENCFF760VJL.w5 128 32 2.0 mean 1845 CHIP:H3K27me3:C57BL/6 forebrain embryo (13.5 days) +1846 ENCFF075BNF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR737JHU/summary/ENCFF075BNF.w5 128 32 2.0 mean 1846 CHIP:H3K9me3:C57BL/6 forebrain embryo (10.5 days) +1847 ENCFF008XYM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR737QWV/summary/ENCFF008XYM.w5 128 32 2.0 mean 1847 CHIP:H3K27ac:C57BL/6 limb embryo (12.5 days) +1848 ENCFF880ZZM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR739DVM/summary/ENCFF880ZZM.w5 128 32 2.0 mean 1848 CHIP:H3K4me3:C57BL/6 forebrain embryo (11.5 days) +1849 ENCFF201DBX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR740DYF/summary/ENCFF201DBX.w5 128 32 2.0 mean 1849 CHIP:H3K27me3:C57BL/6 kidney embryo (15.5 days) +1850 ENCFF113RHY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR743ZJL/summary/ENCFF113RHY.w5 128 32 2.0 mean 1850 CHIP:IRF4:B10.H-2aH-4bp/Wts CH12.LX +1851 ENCFF209EYY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR744LCN/summary/ENCFF209EYY.w5 128 32 2.0 mean 1851 CHIP:H3K9ac:C57BL/6 lung embryo (15.5 days) +1852 ENCFF652SDD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR747VPY/summary/ENCFF652SDD.w5 128 32 2.0 mean 1852 CHIP:H3K4me2:C57BL/6 heart embryo (16.5 days) +1853 ENCFF102KDV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR747ZXL/summary/ENCFF102KDV.w5 128 32 2.0 mean 1853 CHIP:H3K36me3:C57BL/6 midbrain embryo (10.5 days) +1854 ENCFF311RNJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR748BQH/summary/ENCFF311RNJ.w5 128 32 2.0 mean 1854 CHIP:H3K4me2:C57BL/6 heart embryo (11.5 days) +1855 ENCFF463JGO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR749PZB/summary/ENCFF463JGO.w5 128 32 2.0 mean 1855 CHIP:H3K9ac:C57BL/6 intestine embryo (16.5 days) +1856 ENCFF870LES /home/drk/tillage/datasets/mouse/chip/encode/ENCSR751AAB/summary/ENCFF870LES.w5 128 32 2.0 mean 1856 CHIP:H3K4me1:C57BL/6 limb embryo (12.5 days) +1857 ENCFF702AEO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR751HEG/summary/ENCFF702AEO.w5 128 32 2.0 mean 1857 CHIP:H3K9ac:C57BL/6 heart embryo (11.5 days) +1858 ENCFF878NXY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR754AXU/summary/ENCFF878NXY.w5 128 32 2.0 mean 1858 CHIP:H3K9me3:C57BL/6 midbrain embryo (13.5 days) +1859 ENCFF055NHC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR755PMX/summary/ENCFF055NHC.w5 128 32 2.0 mean 1859 CHIP:H3K9ac:C57BL/6 embryonic facial prominence embryo (15.5 days) +1860 ENCFF374BEH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR755SGK/summary/ENCFF374BEH.w5 128 32 2.0 mean 1860 CHIP:H3K4me2:C57BL/6 midbrain embryo (14.5 days) +1861 ENCFF749LHU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR758FWH/summary/ENCFF749LHU.w5 128 32 2.0 mean 1861 CHIP:H3K27me3:C57BL/6 lung embryo (16.5 days) +1862 ENCFF173LCU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR758UAI/summary/ENCFF173LCU.w5 128 32 2.0 mean 1862 CHIP:H3K4me2:C57BL/6 embryonic facial prominence embryo (13.5 days) +1863 ENCFF084MIV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR759RVE/summary/ENCFF084MIV.w5 128 32 2.0 mean 1863 CHIP:H3K4me2:C57BL/6 limb embryo (13.5 days) +1864 ENCFF741GHS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR764UIE/summary/ENCFF741GHS.w5 128 32 2.0 mean 1864 CHIP:H3K36me3:C57BL/6 midbrain embryo (12.5 days) +1865 ENCFF675TVC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR765JWZ/summary/ENCFF675TVC.w5 128 32 2.0 mean 1865 CHIP:H3K4me3:C57BL/6 embryonic facial prominence embryo (10.5 days) +1866 ENCFF251ZXL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR765RPR/summary/ENCFF251ZXL.w5 128 32 2.0 mean 1866 CHIP:EP300:C57BL/6 liver postnatal (0 days) +1867 ENCFF014HTI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR765SJF/summary/ENCFF014HTI.w5 128 32 2.0 mean 1867 CHIP:H3K27me3:C57BL/6 limb embryo (14.5 days) +1868 ENCFF432ADZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR765UOU/summary/ENCFF432ADZ.w5 128 32 2.0 mean 1868 CHIP:H3K9me3:C57BL/6 midbrain embryo (12.5 days) +1869 ENCFF190AYI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR769ITO/summary/ENCFF190AYI.w5 128 32 2.0 mean 1869 CHIP:H3K9me3:C57BL/6 midbrain embryo (10.5 days) +1870 ENCFF335NBL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR770OXU/summary/ENCFF335NBL.w5 128 32 2.0 mean 1870 CHIP:H3K4me1:C57BL/6 liver embryo (12.5 days) +1871 ENCFF035FHN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR771ILS/summary/ENCFF035FHN.w5 128 32 2.0 mean 1871 CHIP:H3K4me2:C57BL/6 hindbrain postnatal (0 days) +1872 ENCFF368BVK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR773EGV/summary/ENCFF368BVK.w5 128 32 2.0 mean 1872 CHIP:H3K9me3:C57BL/6 lung embryo (15.5 days) +1873 ENCFF713BVE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR776QRL/summary/ENCFF713BVE.w5 128 32 2.0 mean 1873 CHIP:H3K36me3:C57BL/6 neural tube embryo (14.5 days) +1874 ENCFF110NKA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR776RJR/summary/ENCFF110NKA.w5 128 32 2.0 mean 1874 CHIP:H3K36me3:C57BL/6 lung embryo (15.5 days) +1875 ENCFF338GTZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR777VNA/summary/ENCFF338GTZ.w5 128 32 2.0 mean 1875 CHIP:EP300:C57BL/6 heart postnatal (0 days) +1876 ENCFF232UNC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR779CZG/summary/ENCFF232UNC.w5 128 32 2.0 mean 1876 CHIP:NANOG:129 E14TG2a.4 +1877 ENCFF442KVI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR779MSI/summary/ENCFF442KVI.w5 128 32 2.0 mean 1877 CHIP:H3K9me3:C57BL/6 embryonic facial prominence embryo (10.5 days) +1878 ENCFF582THV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR780NWL/summary/ENCFF582THV.w5 128 32 2.0 mean 1878 CHIP:H3K9ac:C57BL/6 embryonic facial prominence embryo (13.5 days) +1879 ENCFF280UTR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR781ORQ/summary/ENCFF280UTR.w5 128 32 2.0 mean 1879 CHIP:H3K27me3:C57BL/6 heart embryo (16.5 days) +1880 ENCFF889KFS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR782DEA/summary/ENCFF889KFS.w5 128 32 2.0 mean 1880 CHIP:H3K4me3:C57BL/6 heart embryo (10.5 days) +1881 ENCFF513MGM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR782DGO/summary/ENCFF513MGM.w5 128 32 2.0 mean 1881 CHIP:H3K4me1:C57BL/6 heart embryo (10.5 days) +1882 ENCFF660OFZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR782SUW/summary/ENCFF660OFZ.w5 128 32 2.0 mean 1882 CHIP:H3K4me2:C57BL/6 forebrain embryo (12.5 days) +1883 ENCFF631JYQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR784TLR/summary/ENCFF631JYQ.w5 128 32 2.0 mean 1883 CHIP:H3K27ac:C57BL/6 hindbrain embryo (12.5 days) +1884 ENCFF845OXU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR790LOX/summary/ENCFF845OXU.w5 128 32 2.0 mean 1884 CHIP:H3K27me3:C57BL/6 heart postnatal (0 days) +1885 ENCFF164OJX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR795UOC/summary/ENCFF164OJX.w5 128 32 2.0 mean 1885 CHIP:H3K9ac:C57BL/6 liver embryo (16.5 days) +1886 ENCFF011VMX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR797EYS/summary/ENCFF011VMX.w5 128 32 2.0 mean 1886 CHIP:H3K27ac:C57BL/6 hindbrain embryo (16.5 days) +1887 ENCFF094RXG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR798VHN/summary/ENCFF094RXG.w5 128 32 2.0 mean 1887 CHIP:H3K9ac:C57BL/6 stomach embryo (16.5 days) +1888 ENCFF526VAG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR802RET/summary/ENCFF526VAG.w5 128 32 2.0 mean 1888 CHIP:H3K27ac:C57BL/6 liver embryo (16.5 days) +1889 ENCFF199YQB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR806JZK/summary/ENCFF199YQB.w5 128 32 2.0 mean 1889 CHIP:MEF2A:B10.H-2aH-4bp/Wts CH12.LX +1890 ENCFF032RGE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR809NWL/summary/ENCFF032RGE.w5 128 32 2.0 mean 1890 CHIP:H3K36me3:C57BL/6 hindbrain embryo (15.5 days) +1891 ENCFF623CRW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR810EOA/summary/ENCFF623CRW.w5 128 32 2.0 mean 1891 CHIP:H3K4me1:C57BL/6 limb embryo (15.5 days) +1892 ENCFF596BHZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR813SCQ/summary/ENCFF596BHZ.w5 128 32 2.0 mean 1892 CHIP:H3K27ac:C57BL/6 embryonic facial prominence embryo (12.5 days) +1893 ENCFF767LND /home/drk/tillage/datasets/mouse/chip/encode/ENCSR821GHK/summary/ENCFF767LND.w5 128 32 2.0 mean 1893 CHIP:H3K9me3:C57BL/6 kidney embryo (16.5 days) +1894 ENCFF451RNW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR825OWH/summary/ENCFF451RNW.w5 128 32 2.0 mean 1894 CHIP:H3K4me1:C57BL/6 lung embryo (14.5 days) +1895 ENCFF266KHC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR825ZJV/summary/ENCFF266KHC.w5 128 32 2.0 mean 1895 CHIP:H3K27ac:C57BL/6 forebrain embryo (10.5 days) +1896 ENCFF555JQE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR826TJQ/summary/ENCFF555JQE.w5 128 32 2.0 mean 1896 CHIP:H3K4me1:C57BL/6 neural tube embryo (15.5 days) +1897 ENCFF702GVB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR829YGD/summary/ENCFF702GVB.w5 128 32 2.0 mean 1897 CHIP:H3K4me1:C57BL/6 intestine embryo (16.5 days) +1898 ENCFF074EMQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR831EKS/summary/ENCFF074EMQ.w5 128 32 2.0 mean 1898 CHIP:H3K4me2:C57BL/6 hindbrain embryo (15.5 days) +1899 ENCFF900BKA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR831YAX/summary/ENCFF900BKA.w5 128 32 2.0 mean 1899 CHIP:H3K27me3:C57BL/6 forebrain embryo (14.5 days) +1900 ENCFF314QNW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR835BZO/summary/ENCFF314QNW.w5 128 32 2.0 mean 1900 CHIP:H3K4me3:C57BL/6 forebrain embryo (13.5 days) +1901 ENCFF637PDW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR837SKW/summary/ENCFF637PDW.w5 128 32 2.0 mean 1901 CHIP:H3K27me3:C57BL/6 hindbrain embryo (13.5 days) +1902 ENCFF916AGC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR839WFP/summary/ENCFF916AGC.w5 128 32 2.0 mean 1902 CHIP:H3K4me3:C57BL/6 lung embryo (14.5 days) +1903 ENCFF906TTD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR840QFC/summary/ENCFF906TTD.w5 128 32 2.0 mean 1903 CHIP:H3K36me3:C57BL/6 heart embryo (12.5 days) +1904 ENCFF801FFG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR846PJO/summary/ENCFF801FFG.w5 128 32 2.0 mean 1904 CHIP:H3K27ac:C57BL/6 heart embryo (16.5 days) +1905 ENCFF477UFW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR846ZCW/summary/ENCFF477UFW.w5 128 32 2.0 mean 1905 CHIP:H3K9me3:C57BL/6 liver embryo (11.5 days) +1906 ENCFF736SAK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR846ZTT/summary/ENCFF736SAK.w5 128 32 2.0 mean 1906 CHIP:H3K4me2:C57BL/6 kidney embryo (16.5 days) +1907 ENCFF550PJQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR855NKG/summary/ENCFF550PJQ.w5 128 32 2.0 mean 1907 CHIP:H3K9me3:C57BL/6 liver embryo (15.5 days) +1908 ENCFF376ZJO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR857GQI/summary/ENCFF376ZJO.w5 128 32 2.0 mean 1908 CHIP:H3K27me3:C57BL/6 midbrain embryo (15.5 days) +1909 ENCFF289ATH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR857MYS/summary/ENCFF289ATH.w5 128 32 2.0 mean 1909 CHIP:H3K9me3:129 E14TG2a.4 +1910 ENCFF283EBS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR858AUB/summary/ENCFF283EBS.w5 128 32 2.0 mean 1910 CHIP:H3K4me1:C57BL/6 lung embryo (15.5 days) +1911 ENCFF024LWP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR861MUP/summary/ENCFF024LWP.w5 128 32 2.0 mean 1911 CHIP:H3K27me3:C57BL/6 lung embryo (15.5 days) +1912 ENCFF502YGZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR863VHE/summary/ENCFF502YGZ.w5 128 32 2.0 mean 1912 CHIP:H3K27ac:C57BL/6 limb embryo (10.5 days) +1913 ENCFF377LTJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR864DSI/summary/ENCFF377LTJ.w5 128 32 2.0 mean 1913 CHIP:H3K9me3:C57BL/6 midbrain embryo (15.5 days) +1914 ENCFF462IYV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR864OWV/summary/ENCFF462IYV.w5 128 32 2.0 mean 1914 CHIP:H3K36me3:C57BL/6 hindbrain embryo (16.5 days) +1915 ENCFF345KLB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR868FWZ/summary/ENCFF345KLB.w5 128 32 2.0 mean 1915 CHIP:H3K9ac:C57BL/6 liver embryo (13.5 days) +1916 ENCFF706SAT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR871CGP/summary/ENCFF706SAT.w5 128 32 2.0 mean 1916 CHIP:H3K36me3:C57BL/6 limb embryo (14.5 days) +1917 ENCFF270YCY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR871KVM/summary/ENCFF270YCY.w5 128 32 2.0 mean 1917 CHIP:H3K27me3:C57BL/6 intestine embryo (15.5 days) +1918 ENCFF923CRK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR871YCT/summary/ENCFF923CRK.w5 128 32 2.0 mean 1918 CHIP:H3K36me3:C57BL/6 limb embryo (11.5 days) +1919 ENCFF454YLV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR872WGX/summary/ENCFF454YLV.w5 128 32 2.0 mean 1919 CHIP:H3K36me3:C57BL/6 stomach embryo (16.5 days) +1920 ENCFF059NRZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR875KRK/summary/ENCFF059NRZ.w5 128 32 2.0 mean 1920 CHIP:H3K4me1:C57BL/6 forebrain embryo (15.5 days) +1921 ENCFF104GKL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR875ZAO/summary/ENCFF104GKL.w5 128 32 2.0 mean 1921 CHIP:H3K4me3:C57BL/6 heart postnatal (0 days) +1922 ENCFF665XFW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR883ASH/summary/ENCFF665XFW.w5 128 32 2.0 mean 1922 CHIP:H3K4me1:C57BL/6 kidney embryo (16.5 days) +1923 ENCFF924XGB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR884MYD/summary/ENCFF924XGB.w5 128 32 2.0 mean 1923 CHIP:H3K27ac:C57BL/6 lung postnatal (0 days) +1924 ENCFF911YHS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR886DWH/summary/ENCFF911YHS.w5 128 32 2.0 mean 1924 CHIP:H3K4me2:C57BL/6 embryonic facial prominence embryo (14.5 days) +1925 ENCFF917SXQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR886IHN/summary/ENCFF917SXQ.w5 128 32 2.0 mean 1925 CHIP:H3K4me1:C57BL/6 heart embryo (11.5 days) +1926 ENCFF720WRB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR889MYY/summary/ENCFF720WRB.w5 128 32 2.0 mean 1926 CHIP:H3K9ac:C57BL/6 liver embryo (15.5 days) +1927 ENCFF704GSX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR891SAW/summary/ENCFF704GSX.w5 128 32 2.0 mean 1927 CHIP:H3K27ac:C57BL/6 neural tube embryo (12.5 days) +1928 ENCFF052RHA /home/drk/tillage/datasets/mouse/chip/encode/ENCSR894JAS/summary/ENCFF052RHA.w5 128 32 2.0 mean 1928 CHIP:H3K9me3:C57BL/6 forebrain embryo (11.5 days) +1929 ENCFF018LWM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR895BMP/summary/ENCFF018LWM.w5 128 32 2.0 mean 1929 CHIP:H3K27ac:C57BL/6 lung embryo (15.5 days) +1930 ENCFF897QOI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR897WBY/summary/ENCFF897QOI.w5 128 32 2.0 mean 1930 CHIP:H3K27ac:C57BL/6 limb embryo (11.5 days) +1931 ENCFF753BLB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR898WIS/summary/ENCFF753BLB.w5 128 32 2.0 mean 1931 CHIP:H3K9ac:C57BL/6 liver embryo (14.5 days) +1932 ENCFF402FVP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR905FFU/summary/ENCFF402FVP.w5 128 32 2.0 mean 1932 CHIP:H3K27ac:C57BL/6 limb embryo (13.5 days) +1933 ENCFF177GZH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR906QEK/summary/ENCFF177GZH.w5 128 32 2.0 mean 1933 CHIP:TCF12:B10.H-2aH-4bp/Wts CH12.LX +1934 ENCFF217MZD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR906RTN/summary/ENCFF217MZD.w5 128 32 2.0 mean 1934 CHIP:H3K27me3:C57BL/6 limb embryo (10.5 days) +1935 ENCFF924CKT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR906UJW/summary/ENCFF924CKT.w5 128 32 2.0 mean 1935 CHIP:H3K4me2:C57BL/6 forebrain postnatal (0 days) +1936 ENCFF043PGB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR907CPZ/summary/ENCFF043PGB.w5 128 32 2.0 mean 1936 CHIP:H3K4me1:C57BL/6 stomach embryo (16.5 days) +1937 ENCFF586VVE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR912IXU/summary/ENCFF586VVE.w5 128 32 2.0 mean 1937 CHIP:H3K9ac:C57BL/6 kidney embryo (16.5 days) +1938 ENCFF091TEN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR914QGB/summary/ENCFF091TEN.w5 128 32 2.0 mean 1938 CHIP:H3K4me1:C57BL/6 embryonic facial prominence embryo (10.5 days) +1939 ENCFF703KOJ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR916CBN/summary/ENCFF703KOJ.w5 128 32 2.0 mean 1939 CHIP:H3K4me3:C57BL/6 stomach postnatal (0 days) +1940 ENCFF254FBD /home/drk/tillage/datasets/mouse/chip/encode/ENCSR918ZSJ/summary/ENCFF254FBD.w5 128 32 2.0 mean 1940 CHIP:H3K4me1:C57BL/6 neural tube embryo (13.5 days) +1941 ENCFF815RWW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR919DDC/summary/ENCFF815RWW.w5 128 32 2.0 mean 1941 CHIP:H3K36me3:C57BL/6 intestine embryo (15.5 days) +1942 ENCFF632RYE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR921ILW/summary/ENCFF632RYE.w5 128 32 2.0 mean 1942 CHIP:H3K4me1:C57BL/6 hindbrain embryo (15.5 days) +1943 ENCFF045FHU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR924FJQ/summary/ENCFF045FHU.w5 128 32 2.0 mean 1943 CHIP:H3K4me2:C57BL/6 lung embryo (14.5 days) +1944 ENCFF703BHN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR928CYU/summary/ENCFF703BHN.w5 128 32 2.0 mean 1944 CHIP:H3K4me3:C57BL/6 hindbrain embryo (11.5 days) +1945 ENCFF386EYG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR928IYZ/summary/ENCFF386EYG.w5 128 32 2.0 mean 1945 CHIP:H3K27me3:C57BL/6 neural tube embryo (15.5 days) +1946 ENCFF908XOQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR929GXP/summary/ENCFF908XOQ.w5 128 32 2.0 mean 1946 CHIP:H3K27me3:C57BL/6 midbrain embryo (14.5 days) +1947 ENCFF604BOY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR929SEW/summary/ENCFF604BOY.w5 128 32 2.0 mean 1947 CHIP:H3K27ac:C57BL/6 stomach embryo (15.5 days) +1948 ENCFF197JHX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR930AFR/summary/ENCFF197JHX.w5 128 32 2.0 mean 1948 CHIP:H3K9me3:C57BL/6 neural tube embryo (12.5 days) +1949 ENCFF559KOX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR932BNP/summary/ENCFF559KOX.w5 128 32 2.0 mean 1949 CHIP:H3K36me3:C57BL/6 liver embryo (11.5 days) +1950 ENCFF840MYF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR938MUD/summary/ENCFF840MYF.w5 128 32 2.0 mean 1950 CHIP:H3K4me3:C57BL/6 limb embryo (12.5 days) +1951 ENCFF629BDF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR940CMI/summary/ENCFF629BDF.w5 128 32 2.0 mean 1951 CHIP:H3K4me1:C57BL/6 stomach postnatal (0 days) +1952 ENCFF951TKF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR943QUH/summary/ENCFF951TKF.w5 128 32 2.0 mean 1952 CHIP:H3K9me3:C57BL/6 limb embryo (12.5 days) +1953 ENCFF375ONW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR944XPB/summary/ENCFF375ONW.w5 128 32 2.0 mean 1953 CHIP:H3K27me3:C57BL/6 forebrain embryo (11.5 days) +1954 ENCFF039QOO /home/drk/tillage/datasets/mouse/chip/encode/ENCSR946JEA/summary/ENCFF039QOO.w5 128 32 2.0 mean 1954 CHIP:H3K27me3:C57BL/6 stomach embryo (16.5 days) +1955 ENCFF224IHW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR946RLM/summary/ENCFF224IHW.w5 128 32 2.0 mean 1955 CHIP:H3K9ac:C57BL/6 intestine postnatal (0 days) +1956 ENCFF672TTE /home/drk/tillage/datasets/mouse/chip/encode/ENCSR947QOH/summary/ENCFF672TTE.w5 128 32 2.0 mean 1956 CHIP:H3K4me2:C57BL/6 hindbrain embryo (13.5 days) +1957 ENCFF583JQM /home/drk/tillage/datasets/mouse/chip/encode/ENCSR948RYN/summary/ENCFF583JQM.w5 128 32 2.0 mean 1957 CHIP:H3K9ac:C57BL/6 liver embryo (11.5 days) +1958 ENCFF966CDF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR948VPV/summary/ENCFF966CDF.w5 128 32 2.0 mean 1958 CHIP:H3K9me3:C57BL/6 midbrain embryo (14.5 days) +1959 ENCFF446FGV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR951UWY/summary/ENCFF446FGV.w5 128 32 2.0 mean 1959 CHIP:H3K36me3:C57BL/6 midbrain postnatal (0 days) +1960 ENCFF455WJT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR953HNY/summary/ENCFF455WJT.w5 128 32 2.0 mean 1960 CHIP:H3K4me3:C57BL/6 kidney embryo (16.5 days) +1961 ENCFF224DGI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR953KTY/summary/ENCFF224DGI.w5 128 32 2.0 mean 1961 CHIP:H3K36me3:C57BL/6 intestine embryo (14.5 days) +1962 ENCFF787DNX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR953LFI/summary/ENCFF787DNX.w5 128 32 2.0 mean 1962 CHIP:H3K27me3:C57BL/6 hindbrain embryo (14.5 days) +1963 ENCFF802SIF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR956ZCG/summary/ENCFF802SIF.w5 128 32 2.0 mean 1963 CHIP:H3K9ac:C57BL/6 heart embryo (15.5 days) +1964 ENCFF937IQZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR961MEP/summary/ENCFF937IQZ.w5 128 32 2.0 mean 1964 CHIP:H3K9me3:C57BL/6 limb embryo (11.5 days) +1965 ENCFF420WNH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR961PNM/summary/ENCFF420WNH.w5 128 32 2.0 mean 1965 CHIP:H3K9ac:C57BL/6 kidney embryo (15.5 days) +1966 ENCFF996XRG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR962MBB/summary/ENCFF996XRG.w5 128 32 2.0 mean 1966 CHIP:H3K36me3:C57BL/6 hindbrain embryo (10.5 days) +1967 ENCFF551QTH /home/drk/tillage/datasets/mouse/chip/encode/ENCSR963OLG/summary/ENCFF551QTH.w5 128 32 2.0 mean 1967 CHIP:H3K27me3:C57BL/6 heart embryo (11.5 days) +1968 ENCFF708MBZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR964RRJ/summary/ENCFF708MBZ.w5 128 32 2.0 mean 1968 CHIP:H3K9ac:C57BL/6 embryonic facial prominence embryo (14.5 days) +1969 ENCFF046SEF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR965JWF/summary/ENCFF046SEF.w5 128 32 2.0 mean 1969 CHIP:H3K9me3:C57BL/6 heart postnatal (0 days) +1970 ENCFF541IJI /home/drk/tillage/datasets/mouse/chip/encode/ENCSR966AIB/summary/ENCFF541IJI.w5 128 32 2.0 mean 1970 CHIP:H3K27ac:C57BL/6 forebrain embryo (12.5 days) +1971 ENCFF483COK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR966RAG/summary/ENCFF483COK.w5 128 32 2.0 mean 1971 CHIP:H3K9ac:C57BL/6 liver postnatal (0 days) +1972 ENCFF293RMV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR966TCN/summary/ENCFF293RMV.w5 128 32 2.0 mean 1972 CHIP:H3K27me3:C57BL/6 midbrain embryo (10.5 days) +1973 ENCFF566GYY /home/drk/tillage/datasets/mouse/chip/encode/ENCSR968NPX/summary/ENCFF566GYY.w5 128 32 2.0 mean 1973 CHIP:H3K9ac:C57BL/6 heart embryo (12.5 days) +1974 ENCFF587CHP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR969CPK/summary/ENCFF587CHP.w5 128 32 2.0 mean 1974 CHIP:H3K27me3:C57BL/6 stomach postnatal (0 days) +1975 ENCFF703RAT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR969NXN/summary/ENCFF703RAT.w5 128 32 2.0 mean 1975 CHIP:H3K36me3:C57BL/6 lung embryo (16.5 days) +1976 ENCFF063VTT /home/drk/tillage/datasets/mouse/chip/encode/ENCSR972LUE/summary/ENCFF063VTT.w5 128 32 2.0 mean 1976 CHIP:H3K9me3:C57BL/6 hindbrain embryo (12.5 days) +1977 ENCFF789SIC /home/drk/tillage/datasets/mouse/chip/encode/ENCSR972MRN/summary/ENCFF789SIC.w5 128 32 2.0 mean 1977 CHIP:H3K36me3:DBA/2 MEL cell line +1978 ENCFF330KGP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR972MUO/summary/ENCFF330KGP.w5 128 32 2.0 mean 1978 CHIP:H3K36me3:C57BL/6 hindbrain embryo (13.5 days) +1979 ENCFF230BUR /home/drk/tillage/datasets/mouse/chip/encode/ENCSR972WEN/summary/ENCFF230BUR.w5 128 32 2.0 mean 1979 CHIP:H3K4me1:C57BL/6 embryonic facial prominence embryo (14.5 days) +1980 ENCFF237WUZ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR973AYQ/summary/ENCFF237WUZ.w5 128 32 2.0 mean 1980 CHIP:H3K4me2:C57BL/6 neural tube embryo (13.5 days) +1981 ENCFF193AYX /home/drk/tillage/datasets/mouse/chip/encode/ENCSR973SOG/summary/ENCFF193AYX.w5 128 32 2.0 mean 1981 CHIP:USF1:B10.H-2aH-4bp/Wts CH12.LX +1982 ENCFF633GEF /home/drk/tillage/datasets/mouse/chip/encode/ENCSR973UGS/summary/ENCFF633GEF.w5 128 32 2.0 mean 1982 CHIP:H3K27me3:C57BL/6 liver postnatal (0 days) +1983 ENCFF417JCK /home/drk/tillage/datasets/mouse/chip/encode/ENCSR975QEX/summary/ENCFF417JCK.w5 128 32 2.0 mean 1983 CHIP:H3K9me3:C57BL/6 stomach embryo (15.5 days) +1984 ENCFF260BXV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR975QSF/summary/ENCFF260BXV.w5 128 32 2.0 mean 1984 CHIP:H3K4me1:C57BL/6 forebrain embryo (11.5 days) +1985 ENCFF968CFU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR976GSO/summary/ENCFF968CFU.w5 128 32 2.0 mean 1985 CHIP:H3K9me3:C57BL/6 stomach embryo (14.5 days) +1986 ENCFF127DNN /home/drk/tillage/datasets/mouse/chip/encode/ENCSR977DCO/summary/ENCFF127DNN.w5 128 32 2.0 mean 1986 CHIP:H3K4me1:C57BL/6 neural tube embryo (14.5 days) +1987 ENCFF650BRL /home/drk/tillage/datasets/mouse/chip/encode/ENCSR980YXJ/summary/ENCFF650BRL.w5 128 32 2.0 mean 1987 CHIP:NRF1:B10.H-2aH-4bp/Wts CH12.LX +1988 ENCFF549QHQ /home/drk/tillage/datasets/mouse/chip/encode/ENCSR982LJQ/summary/ENCFF549QHQ.w5 128 32 2.0 mean 1988 CHIP:EP300:C57BL/6 liver embryo (14.5 days) +1989 ENCFF898VDV /home/drk/tillage/datasets/mouse/chip/encode/ENCSR984OHL/summary/ENCFF898VDV.w5 128 32 2.0 mean 1989 CHIP:H3K27me3:C57BL/6 hindbrain embryo (10.5 days) +1990 ENCFF068KSP /home/drk/tillage/datasets/mouse/chip/encode/ENCSR985UTP/summary/ENCFF068KSP.w5 128 32 2.0 mean 1990 CHIP:H3K4me3:C57BL/6 liver embryo (13.5 days) +1991 ENCFF581XWU /home/drk/tillage/datasets/mouse/chip/encode/ENCSR985ZTV/summary/ENCFF581XWU.w5 128 32 2.0 mean 1991 CHIP:CTCF:C57BL/6 midbrain postnatal (0 days) +1992 ENCFF199SCG /home/drk/tillage/datasets/mouse/chip/encode/ENCSR988BRP/summary/ENCFF199SCG.w5 128 32 2.0 mean 1992 CHIP:H3K27ac:C57BL/6 limb embryo (15.5 days) +1993 ENCFF773NIS /home/drk/tillage/datasets/mouse/chip/encode/ENCSR989LUY/summary/ENCFF773NIS.w5 128 32 2.0 mean 1993 CHIP:H3K27ac:C57BL/6 midbrain embryo (10.5 days) +1994 ENCFF727YWB /home/drk/tillage/datasets/mouse/chip/encode/ENCSR990JMN/summary/ENCFF727YWB.w5 128 32 2.0 mean 1994 CHIP:H3K4me3:C57BL/6 embryonic facial prominence embryo (15.5 days) +1995 ENCFF739NQW /home/drk/tillage/datasets/mouse/chip/encode/ENCSR992SHK/summary/ENCFF739NQW.w5 128 32 2.0 mean 1995 CHIP:H3K4me1:C57BL/6 forebrain embryo (10.5 days) +1996 GSM1094254 /home/drk/tillage/datasets/mouse/chip/geo/GSM1094254/summary/coverage.w5 256 64 1.0 sum 1996 CHIP:CEBPb:CEBPB_ChIP-seq / CEBPB_ChIP-seq / Primary dermal fibroblasts +1997 GSM1094255 /home/drk/tillage/datasets/mouse/chip/geo/GSM1094255/summary/coverage.w5 256 64 1.0 sum 1997 CHIP:CEBPb:CEBPB_Tg_ChIP-seq / CEBPB_Tg_ChIP-seq / Primary dermal fibroblasts +1998 GSM1094256 /home/drk/tillage/datasets/mouse/chip/geo/GSM1094256/summary/coverage.w5 256 64 1.0 sum 1998 CHIP:ATF4:ATF4_ChIP-seq / ATF4_ChIP-seq / Primary dermal fibroblasts +1999 GSM1176709 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176709/summary/coverage.w5 256 64 1.0 sum 1999 CHIP:SREBP1:SREBP1 (ZT02) / SREBP1_ZT02, liver cells / . +2000 GSM1176710 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176710/summary/coverage.w5 256 64 1.0 sum 2000 CHIP:SREBP1:SREBP1 (ZT06) / SREBP1_ZT06, liver cells / . +2001 GSM1176711 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176711/summary/coverage.w5 256 64 1.0 sum 2001 CHIP:SREBP1:SREBP1 (ZT10) / SREBP1_ZT10, liver cells / . +2002 GSM1176712 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176712/summary/coverage.w5 256 64 1.0 sum 2002 CHIP:SREBP1:SREBP1 (ZT14) / SREBP1_ZT14, liver cells / . +2003 GSM1176713 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176713/summary/coverage.w5 256 64 1.0 sum 2003 CHIP:SREBP1:SREBP1 (ZT18) / SREBP1_ZT18, liver cells / . +2004 GSM1176714 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176714/summary/coverage.w5 256 64 1.0 sum 2004 CHIP:SREBP1:SREBP1 (ZT22) / SREBP1_ZT22, liver cells / . +2005 GSM1176721 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176721/summary/coverage.w5 256 64 1.0 sum 2005 CHIP:RPB2:Polr2b (ZT02) / RPB2_ZT02, liver cells / . +2006 GSM1176722 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176722/summary/coverage.w5 256 64 1.0 sum 2006 CHIP:RPB2:Polr2b (ZT06) / RPB2_ZT06, liver cells / . +2007 GSM1176723 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176723/summary/coverage.w5 256 64 1.0 sum 2007 CHIP:RPB2:Polr2b (ZT10) / RPB2_ZT10, liver cells / . +2008 GSM1176724 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176724/summary/coverage.w5 256 64 1.0 sum 2008 CHIP:RPB2:Polr2b (ZT14) / RPB2_ZT14, liver cells / . +2009 GSM1176725 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176725/summary/coverage.w5 256 64 1.0 sum 2009 CHIP:RPB2:Polr2b (ZT18) / RPB2_ZT18, liver cells / . +2010 GSM1176726 /home/drk/tillage/datasets/mouse/chip/geo/GSM1176726/summary/coverage.w5 256 64 1.0 sum 2010 CHIP:RPB2:Polr2b (ZT22) / RPB2_ZT22, liver cells / . +2011 GSM1198156 /home/drk/tillage/datasets/mouse/chip/geo/GSM1198156/summary/coverage.w5 256 64 1.0 sum 2011 CHIP:H3K9ac:H3K9ac ChIPSeq Cre_cohort1 / H3K9ac ChIPSeq Cre_cohort1 / . +2012 GSM1198157 /home/drk/tillage/datasets/mouse/chip/geo/GSM1198157/summary/coverage.w5 256 64 1.0 sum 2012 CHIP:H3K9ac:H3K9ac ChIPSeq WT_cohort1 / H3K9ac ChIPSeq WT_cohort1 / . +2013 GSM1198158 /home/drk/tillage/datasets/mouse/chip/geo/GSM1198158/summary/coverage.w5 256 64 1.0 sum 2013 CHIP:H3K9ac:H3K9ac ChIPSeq HAHA_cohort1 / H3K9ac ChIPSeq HAHA_cohort1 / . +2014 GSM1198159 /home/drk/tillage/datasets/mouse/chip/geo/GSM1198159/summary/coverage.w5 256 64 1.0 sum 2014 CHIP:H3K9ac:H3K9ac ChIPSeq KA_cohort1 / H3K9ac ChIPSeq KA_cohort1 / . +2015 GSM1198162 /home/drk/tillage/datasets/mouse/chip/geo/GSM1198162/summary/coverage.w5 256 64 1.0 sum 2015 CHIP:H3K9ac:H3K9ac ChIPSeq YF_cohort2 / H3K9ac ChIPSeq YF_cohort2 / . +2016 GSM1198163 /home/drk/tillage/datasets/mouse/chip/geo/GSM1198163/summary/coverage.w5 256 64 1.0 sum 2016 CHIP:H3K9ac:H3K9ac ChIPSeq HEBI_cohort2 / H3K9ac ChIPSeq HEBI_cohort2 / . +2017 GSM1236494 /home/drk/tillage/datasets/mouse/chip/geo/GSM1236494/summary/coverage.w5 256 64 1.0 sum 2017 CHIP:SMRT:SMRT ChIPSeq 5PM (ZT10) / liver / . +2018 GSM1236495 /home/drk/tillage/datasets/mouse/chip/geo/GSM1236495/summary/coverage.w5 256 64 1.0 sum 2018 CHIP:SMRT:SMRT ChIPSeq 5AM (ZT22) / liver / . +2019 GSM1301669 /home/drk/tillage/datasets/mouse/chip/geo/GSM1301669/summary/coverage.w5 256 64 1.0 sum 2019 CHIP:CLOCK:ZT8 CLOCK ChIP Seq-1 / Liver / . +2020 GSM1301671 /home/drk/tillage/datasets/mouse/chip/geo/GSM1301671/summary/coverage.w5 256 64 1.0 sum 2020 CHIP:BMAL1:ZT8 BMAL1 ChIP Seq-1 / Liver / . +2021 GSM1301673 /home/drk/tillage/datasets/mouse/chip/geo/GSM1301673/summary/coverage.w5 256 64 1.0 sum 2021 CHIP:CRY1:ZT20 CRY1 ChIP Seq / Liver / . +2022 GSM1437733 /home/drk/tillage/datasets/mouse/chip/geo/GSM1437733/summary/coverage.w5 256 64 1.0 sum 2022 CHIP:E4BP4:E4BP4 Liver ZT22 ChIP-seq / liver / . +2023 GSM1437734 /home/drk/tillage/datasets/mouse/chip/geo/GSM1437734/summary/coverage.w5 256 64 1.0 sum 2023 CHIP:RORalpha:RORalpha Liver ZT22 ChIP-seq / liver / . +2024 GSM1446062 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446062/summary/coverage.w5 256 64 1.0 sum 2024 CHIP:GR:ChIP-seq, Liver_GR_GRdim_6am / Liver tissue / . +2025 GSM1446063 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446063/summary/coverage.w5 256 64 1.0 sum 2025 CHIP:GR:ChIP-seq, Liver_GR_GRdim_6pm / Liver tissue / . +2026 GSM1446064 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446064/summary/coverage.w5 256 64 1.0 sum 2026 CHIP:GR:ChIP-seq, Liver_GR_GRdim_pred_6am / Liver tissue / . +2027 GSM1446065 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446065/summary/coverage.w5 256 64 1.0 sum 2027 CHIP:GR:ChIP-seq, Liver_GR_WT_6am / Liver tissue / . +2028 GSM1446066 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446066/summary/coverage.w5 256 64 1.0 sum 2028 CHIP:GR:ChIP-seq, Liver_GR_WT_6pm / Liver tissue / . +2029 GSM1446067 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446067/summary/coverage.w5 256 64 1.0 sum 2029 CHIP:GR:ChIP-seq, Liver_GR_WT_pred_6am / Liver tissue / . +2030 GSM1446068 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446068/summary/coverage.w5 256 64 1.0 sum 2030 CHIP:RNAPII:ChIP-seq, Liver_RNAPII_WT_6am / Liver tissue / . +2031 GSM1446069 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446069/summary/coverage.w5 256 64 1.0 sum 2031 CHIP:RNAPII:ChIP-seq, Liver_RNAPII_WT_pred_6am / Liver tissue / . +2032 GSM1446070 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446070/summary/coverage.w5 256 64 1.0 sum 2032 CHIP:CEBPb:ChIP-seq, Liver_CEBPb_WT_6pm / Liver tissue / . +2033 GSM1446071 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446071/summary/coverage.w5 256 64 1.0 sum 2033 CHIP:GR:ChIP-exo, Liver_GR_GRdim_6am / Liver tissue / . +2034 GSM1446072 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446072/summary/coverage.w5 256 64 1.0 sum 2034 CHIP:GR:ChIP-exo, Liver_GR_GRdim_6pm / Liver tissue / . +2035 GSM1446073 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446073/summary/coverage.w5 256 64 1.0 sum 2035 CHIP:GR:ChIP-exo, Liver_GR_GRdim_pred_6am / Liver tissue / . +2036 GSM1446074 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446074/summary/coverage.w5 256 64 1.0 sum 2036 CHIP:GR:ChIP-exo, Liver_GR_WT_6am / Liver tissue / . +2037 GSM1446075 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446075/summary/coverage.w5 256 64 1.0 sum 2037 CHIP:GR:ChIP-exo, Liver_GR_WT_6pm / Liver tissue / . +2038 GSM1446076 /home/drk/tillage/datasets/mouse/chip/geo/GSM1446076/summary/coverage.w5 256 64 1.0 sum 2038 CHIP:GR:ChIP-exo, Liver_GR_WT_pred_6am / Liver tissue / . +2039 GSM1479709 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479709/summary/coverage.w5 256 64 1.0 sum 2039 CHIP:PolII:PolII ZT 2 WT / Liver, WT, ZT 2, PolII ChIP / . +2040 GSM1479710 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479710/summary/coverage.w5 256 64 1.0 sum 2040 CHIP:PolII:PolII ZT 6 WT / Liver, WT, ZT 6, PolII ChIP / . +2041 GSM1479711 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479711/summary/coverage.w5 256 64 1.0 sum 2041 CHIP:PolII:PolII ZT 10 WT / Liver, WT, ZT 10, PolII ChIP / . +2042 GSM1479712 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479712/summary/coverage.w5 256 64 1.0 sum 2042 CHIP:PolII:PolII ZT 14 WT / Liver, WT, ZT 14, PolII ChIP / . +2043 GSM1479713 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479713/summary/coverage.w5 256 64 1.0 sum 2043 CHIP:PolII:PolII ZT 18 WT / Liver, WT, ZT 18, PolII ChIP / . +2044 GSM1479714 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479714/summary/coverage.w5 256 64 1.0 sum 2044 CHIP:PolII:PolII ZT 22 WT / Liver, WT, ZT 22, PolII ChIP / . +2045 GSM1479715 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479715/summary/coverage.w5 256 64 1.0 sum 2045 CHIP:PolII:PolII ZT 26 WT / Liver, WT, ZT 26, PolII ChIP / . +2046 GSM1479716 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479716/summary/coverage.w5 256 64 1.0 sum 2046 CHIP:PolII:PolII ZT 2 Bmal1 KO / Liver, Bmal1 KO, ZT 2, PolII ChIP / . +2047 GSM1479717 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479717/summary/coverage.w5 256 64 1.0 sum 2047 CHIP:PolII:PolII ZT 6 Bmal1 KO / Liver, Bmal1 KO, ZT 6, PolII ChIP / . +2048 GSM1479718 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479718/summary/coverage.w5 256 64 1.0 sum 2048 CHIP:PolII:PolII ZT 10 Bmal1 KO / Liver, Bmal1 KO, ZT 10, PolII ChIP / . +2049 GSM1479719 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479719/summary/coverage.w5 256 64 1.0 sum 2049 CHIP:PolII:PolII ZT 14 Bmal1 KO / Liver, Bmal1 KO, ZT 14, PolII ChIP / . +2050 GSM1479720 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479720/summary/coverage.w5 256 64 1.0 sum 2050 CHIP:PolII:PolII ZT 18 Bmal1 KO / Liver, Bmal1 KO, ZT 18, PolII ChIP / . +2051 GSM1479721 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479721/summary/coverage.w5 256 64 1.0 sum 2051 CHIP:PolII:PolII ZT 22 Bmal1 KO / Liver, Bmal1 KO, ZT 22, PolII ChIP / . +2052 GSM1479722 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479722/summary/coverage.w5 256 64 1.0 sum 2052 CHIP:PolII:PolII ZT 26 Bmal1 KO / Liver, Bmal1 KO, ZT 26, PolII ChIP / . +2053 GSM1479723 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479723/summary/coverage.w5 256 64 1.0 sum 2053 CHIP:H3K27ac:H3K27ac ZT 2 WT / Liver, WT, ZT 2, H3K27ac ChIP / . +2054 GSM1479724 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479724/summary/coverage.w5 256 64 1.0 sum 2054 CHIP:H3K27ac:H3K27ac ZT 6 WT / Liver, WT, ZT 6, H3K27ac ChIP / . +2055 GSM1479725 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479725/summary/coverage.w5 256 64 1.0 sum 2055 CHIP:H3K27ac:H3K27ac ZT 10 WT / Liver, WT, ZT 10, H3K27ac ChIP / . +2056 GSM1479726 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479726/summary/coverage.w5 256 64 1.0 sum 2056 CHIP:H3K27ac:H3K27ac ZT 14 WT / Liver, WT, ZT 14, H3K27ac ChIP / . +2057 GSM1479727 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479727/summary/coverage.w5 256 64 1.0 sum 2057 CHIP:H3K27ac:H3K27ac ZT 18 WT / Liver, WT, ZT 18, H3K27ac ChIP / . +2058 GSM1479728 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479728/summary/coverage.w5 256 64 1.0 sum 2058 CHIP:H3K27ac:H3K27ac ZT 22 WT / Liver, WT, ZT 22, H3K27ac ChIP / . +2059 GSM1479729 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479729/summary/coverage.w5 256 64 1.0 sum 2059 CHIP:H3K27ac:H3K27ac ZT 26 WT / Liver, WT, ZT 26, H3K27ac ChIP / . +2060 GSM1479730 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479730/summary/coverage.w5 256 64 1.0 sum 2060 CHIP:H3K27ac:H3K27ac ZT 2 Bmal1 KO / Liver, Bmal1 KO, ZT 2, H3K27ac ChIP / . +2061 GSM1479731 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479731/summary/coverage.w5 256 64 1.0 sum 2061 CHIP:H3K27ac:H3K27ac ZT 6 Bmal1 KO / Liver, Bmal1 KO, ZT 6, H3K27ac ChIP / . +2062 GSM1479732 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479732/summary/coverage.w5 256 64 1.0 sum 2062 CHIP:H3K27ac:H3K27ac ZT 10 Bmal1 KO / Liver, Bmal1 KO, ZT 10, H3K27ac ChIP / . +2063 GSM1479733 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479733/summary/coverage.w5 256 64 1.0 sum 2063 CHIP:H3K27ac:H3K27ac ZT 14 Bmal1 KO / Liver, Bmal1 KO, ZT 14, H3K27ac ChIP / . +2064 GSM1479734 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479734/summary/coverage.w5 256 64 1.0 sum 2064 CHIP:H3K27ac:H3K27ac ZT 18 Bmal1 KO / Liver, Bmal1 KO, ZT 18, H3K27ac ChIP / . +2065 GSM1479735 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479735/summary/coverage.w5 256 64 1.0 sum 2065 CHIP:H3K27ac:H3K27ac ZT 22 Bmal1 KO / Liver, Bmal1 KO, ZT 22, H3K27ac ChIP / . +2066 GSM1479736 /home/drk/tillage/datasets/mouse/chip/geo/GSM1479736/summary/coverage.w5 256 64 1.0 sum 2066 CHIP:H3K27ac:H3K27ac ZT 26 Bmal1 KO / Liver, Bmal1 KO, ZT 26, H3K27ac ChIP / . +2067 GSM1631168 /home/drk/tillage/datasets/mouse/chip/geo/GSM1631168/summary/coverage.w5 256 64 1.0 sum 2067 CHIP:CEBPb:ChIP-seq, Liver_CEBPb_WT_6am / Liver tissue / . +2068 GSM1631170 /home/drk/tillage/datasets/mouse/chip/geo/GSM1631170/summary/coverage.w5 256 64 1.0 sum 2068 CHIP:CEBPb:ChIP-seq, Liver_CEBPb_WT_pred_6am / Liver tissue / . +2069 GSM1659681 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659681/summary/coverage.w5 256 64 1.0 sum 2069 CHIP:NR1D1:Rev-erbalpha_eWAT_ZT10_rep1 / eWAT / . +2070 GSM1659684 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659684/summary/coverage.w5 256 64 1.0 sum 2070 CHIP:NR1D1:Rev-erbalpha_brain_ZT10 / brain(ventral tegmental area) / . +2071 GSM1659686 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659686/summary/coverage.w5 256 64 1.0 sum 2071 CHIP:NR1D1:Rev-erbalpha_WT_liver_ZT10_rep1 / liver / . +2072 GSM1659688 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659688/summary/coverage.w5 256 64 1.0 sum 2072 CHIP:NR1D1:129mice_WT_liver_ZT10_rep1 / liver / . +2073 GSM1659690 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659690/summary/coverage.w5 256 64 1.0 sum 2073 CHIP:NR1D1:Rev-erbalpha_DBD_mutant_liver_ZT10_rep1 / liver / . +2074 GSM1659692 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659692/summary/coverage.w5 256 64 1.0 sum 2074 CHIP:RORA:RORalpha_liver_ZT10 / liver / . +2075 GSM1659693 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659693/summary/coverage.w5 256 64 1.0 sum 2075 CHIP:RORG:RORgamma_liver_ZT10 / liver / . +2076 GSM1659694 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659694/summary/coverage.w5 256 64 1.0 sum 2076 CHIP:RORG:RORgamma_liver_ZT22 / liver / . +2077 GSM1659695 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659695/summary/coverage.w5 256 64 1.0 sum 2077 CHIP:HDAC3:HDAC3_liver_reverbGFP_ZT10_rep1 / liver / . +2078 GSM1659697 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659697/summary/coverage.w5 256 64 1.0 sum 2078 CHIP:HDAC3:HDAC3_liver_Rev-erbsflCRE(DBDm)_ZT10_rep1 / liver / . +2079 GSM1659699 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659699/summary/coverage.w5 256 64 1.0 sum 2079 CHIP:HDAC3:liver_ZT10 / liver / . +2080 GSM1659700 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659700/summary/coverage.w5 256 64 1.0 sum 2080 CHIP:HDAC3:HDAC3_liver_reverbalphaKO_betaKD_ZT10 / liver / . +2081 GSM1659701 /home/drk/tillage/datasets/mouse/chip/geo/GSM1659701/summary/coverage.w5 256 64 1.0 sum 2081 CHIP:HDAC3:HDAC3_KO_liver_ZT10_rep1 / liver / . +2082 GSM1855803 /home/drk/tillage/datasets/mouse/chip/geo/GSM1855803/summary/coverage.w5 256 64 1.0 sum 2082 CHIP:HSF1:HSF1 ZT14 / Liver / . +2083 GSM2218846 /home/drk/tillage/datasets/mouse/chip/geo/GSM2218846/summary/coverage.w5 256 64 1.0 sum 2083 CHIP:Rev-erba:Rev-erba ChIP-seq at ZT10 (Wild Type) Replicate 1 / liver / . +2084 GSM2218849 /home/drk/tillage/datasets/mouse/chip/geo/GSM2218849/summary/coverage.w5 256 64 1.0 sum 2084 CHIP:Rev-erba:Rev-erba ChIP-seq at ZT10 (HNF6 KO) Replicate 1 / liver / . +2085 GSM2390508 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390508/summary/coverage.w5 256 64 1.0 sum 2085 CHIP:RPC4:ZT02, rep1, CONTROL / Liver / . +2086 GSM2390509 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390509/summary/coverage.w5 256 64 1.0 sum 2086 CHIP:RPC4:ZT06, rep1, CONTROL / Liver / . +2087 GSM2390510 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390510/summary/coverage.w5 256 64 1.0 sum 2087 CHIP:RPC4:ZT10, rep1, CONTROL / Liver / . +2088 GSM2390511 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390511/summary/coverage.w5 256 64 1.0 sum 2088 CHIP:RPC4:ZT14, rep1, CONTROL / Liver / . +2089 GSM2390512 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390512/summary/coverage.w5 256 64 1.0 sum 2089 CHIP:RPC4:ZT18, rep1, CONTROL / Liver / . +2090 GSM2390513 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390513/summary/coverage.w5 256 64 1.0 sum 2090 CHIP:RPC4:ZT22, rep1, CONTROL / Liver / . +2091 GSM2390532 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390532/summary/coverage.w5 256 64 1.0 sum 2091 CHIP:RPC4:ZT02, rep1, CONSTANTLY FED / Liver / . +2092 GSM2390533 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390533/summary/coverage.w5 256 64 1.0 sum 2092 CHIP:RPC4:ZT06, rep1, CONSTANTLY FED / Liver / . +2093 GSM2390534 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390534/summary/coverage.w5 256 64 1.0 sum 2093 CHIP:RPC4:ZT10, rep1, CONSTANTLY FED / Liver / . +2094 GSM2390535 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390535/summary/coverage.w5 256 64 1.0 sum 2094 CHIP:RPC4:ZT14, rep1, CONSTANTLY FED / Liver / . +2095 GSM2390536 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390536/summary/coverage.w5 256 64 1.0 sum 2095 CHIP:RPC4:ZT18, rep1, CONSTANTLY FED / Liver / . +2096 GSM2390537 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390537/summary/coverage.w5 256 64 1.0 sum 2096 CHIP:RPC4:ZT22, rep1, CONSTANTLY FED / Liver / . +2097 GSM2390538 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390538/summary/coverage.w5 256 64 1.0 sum 2097 CHIP:RPC4:ZT26, rep1, CONSTANTLY FED / Liver / . +2098 GSM2390560 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390560/summary/coverage.w5 256 64 1.0 sum 2098 CHIP:RPC4:ZT02, rep1, Arntl KO / Liver / . +2099 GSM2390561 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390561/summary/coverage.w5 256 64 1.0 sum 2099 CHIP:RPC4:ZT06, rep1, Arntl KO / Liver / . +2100 GSM2390562 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390562/summary/coverage.w5 256 64 1.0 sum 2100 CHIP:RPC4:ZT10, rep1, Arntl KO / Liver / . +2101 GSM2390563 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390563/summary/coverage.w5 256 64 1.0 sum 2101 CHIP:RPC4:ZT14, rep1, Arntl KO / Liver / . +2102 GSM2390564 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390564/summary/coverage.w5 256 64 1.0 sum 2102 CHIP:RPC4:ZT18, rep1, Arntl KO / Liver / . +2103 GSM2390565 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390565/summary/coverage.w5 256 64 1.0 sum 2103 CHIP:RPC4:ZT22, rep1, Arntl KO / Liver / . +2104 GSM2390584 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390584/summary/coverage.w5 256 64 1.0 sum 2104 CHIP:RPC4:ZT02, rep1, Maf1 KO / Liver / . +2105 GSM2390585 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390585/summary/coverage.w5 256 64 1.0 sum 2105 CHIP:RPC4:ZT06, rep1, Maf1 KO / Liver / . +2106 GSM2390586 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390586/summary/coverage.w5 256 64 1.0 sum 2106 CHIP:RPC4:ZT10, rep1, Maf1 KO / Liver / . +2107 GSM2390587 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390587/summary/coverage.w5 256 64 1.0 sum 2107 CHIP:RPC4:ZT14, rep1, Maf1 KO / Liver / . +2108 GSM2390588 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390588/summary/coverage.w5 256 64 1.0 sum 2108 CHIP:RPC4:ZT18, rep1, Maf1 KO / Liver / . +2109 GSM2390589 /home/drk/tillage/datasets/mouse/chip/geo/GSM2390589/summary/coverage.w5 256 64 1.0 sum 2109 CHIP:RPC4:ZT22, rep1, Maf1 KO / Liver / . +2110 GSM3212796 /home/drk/tillage/datasets/mouse/chip/geo/GSM3212796/summary/coverage.w5 256 64 1.0 sum 2110 CHIP:BMAL1:ZT4 control rep1 / gastrocnemius / . +2111 GSM3212798 /home/drk/tillage/datasets/mouse/chip/geo/GSM3212798/summary/coverage.w5 256 64 1.0 sum 2111 CHIP:RNA:RNAP2_ZT4 control rep1 / gastrocnemius / . +2112 GSM3212801 /home/drk/tillage/datasets/mouse/chip/geo/GSM3212801/summary/coverage.w5 256 64 1.0 sum 2112 CHIP:Rev-erba:Reverba_ZT8 control REP1 / gastrocnemius / . +2113 GSM647022 /home/drk/tillage/datasets/mouse/chip/geo/GSM647022/summary/coverage.w5 256 64 1.0 sum 2113 CHIP:HDAC3:ZT10-1 / Liver / . +2114 GSM647025 /home/drk/tillage/datasets/mouse/chip/geo/GSM647025/summary/coverage.w5 256 64 1.0 sum 2114 CHIP:HDAC3:ZT22-1 / Liver / . +2115 GSM647027 /home/drk/tillage/datasets/mouse/chip/geo/GSM647027/summary/coverage.w5 256 64 1.0 sum 2115 CHIP:NCoR:ZT10 / Liver / . +2116 GSM647028 /home/drk/tillage/datasets/mouse/chip/geo/GSM647028/summary/coverage.w5 256 64 1.0 sum 2116 CHIP:NCoR:ZT22 / Liver / . +2117 GSM647029 /home/drk/tillage/datasets/mouse/chip/geo/GSM647029/summary/coverage.w5 256 64 1.0 sum 2117 CHIP:NR1D1:ZT10 / Liver / . +2118 GSM647030 /home/drk/tillage/datasets/mouse/chip/geo/GSM647030/summary/coverage.w5 256 64 1.0 sum 2118 CHIP:NR1D1:ZT22 / Liver / . +2119 GSM647031 /home/drk/tillage/datasets/mouse/chip/geo/GSM647031/summary/coverage.w5 256 64 1.0 sum 2119 CHIP:PolII:ZT10 / Liver / . +2120 GSM647032 /home/drk/tillage/datasets/mouse/chip/geo/GSM647032/summary/coverage.w5 256 64 1.0 sum 2120 CHIP:PolII:ZT22 / Liver / . +2121 GSM647035 /home/drk/tillage/datasets/mouse/chip/geo/GSM647035/summary/coverage.w5 256 64 1.0 sum 2121 CHIP:H3K9ac:ZT10 / Liver / . +2122 GSM647036 /home/drk/tillage/datasets/mouse/chip/geo/GSM647036/summary/coverage.w5 256 64 1.0 sum 2122 CHIP:H3K9ac:ZT22 / Liver / . +2123 GSM647037 /home/drk/tillage/datasets/mouse/chip/geo/GSM647037/summary/coverage.w5 256 64 1.0 sum 2123 CHIP:H3K9ac:HDAC3 KO liver at ZT10 / Liver / . +2124 GSM840528 /home/drk/tillage/datasets/mouse/chip/geo/GSM840528/summary/coverage.w5 256 64 1.0 sum 2124 CHIP:REV-ERB:REV-ERB alpha / liver_REV-ERB alpha_ChIP / . +2125 GSM840529 /home/drk/tillage/datasets/mouse/chip/geo/GSM840529/summary/coverage.w5 256 64 1.0 sum 2125 CHIP:REV-ERB:REV-ERB beta / liver_REV-ERB beta_ChIP / . +2126 GSM864668 /home/drk/tillage/datasets/mouse/chip/geo/GSM864668/summary/coverage.w5 256 64 1.0 sum 2126 CHIP:LXR:WT Bexarotene / C57BL/6 wild type mouse liver / . +2127 GSM864669 /home/drk/tillage/datasets/mouse/chip/geo/GSM864669/summary/coverage.w5 256 64 1.0 sum 2127 CHIP:LXR:WT Control / C57BL/6 wild type mouse liver / . +2128 GSM864670 /home/drk/tillage/datasets/mouse/chip/geo/GSM864670/summary/coverage.w5 256 64 1.0 sum 2128 CHIP:LXR:WT T0901317 / C57BL/6 wild type mouse liver / . +2129 GSM864671 /home/drk/tillage/datasets/mouse/chip/geo/GSM864671/summary/coverage.w5 256 64 1.0 sum 2129 CHIP:PPARA:WT Control / C57BL/6 wild type mouse liver / . +2130 GSM864672 /home/drk/tillage/datasets/mouse/chip/geo/GSM864672/summary/coverage.w5 256 64 1.0 sum 2130 CHIP:PPARA:LXRdKO Control / C57BL/6 LXRdKO mouse liver / . +2131 GSM864673 /home/drk/tillage/datasets/mouse/chip/geo/GSM864673/summary/coverage.w5 256 64 1.0 sum 2131 CHIP:RXR:WT Bexarotene / C57BL/6 wild type mouse liver / . +2132 GSM864674 /home/drk/tillage/datasets/mouse/chip/geo/GSM864674/summary/coverage.w5 256 64 1.0 sum 2132 CHIP:RXR:WT Control / C57BL/6 wild type mouse liver / . +2133 GSM864675 /home/drk/tillage/datasets/mouse/chip/geo/GSM864675/summary/coverage.w5 256 64 1.0 sum 2133 CHIP:RXR:WT T0901317 / C57BL/6 wild type mouse liver / . +2134 GSM864676 /home/drk/tillage/datasets/mouse/chip/geo/GSM864676/summary/coverage.w5 256 64 1.0 sum 2134 CHIP:RXR:LXRdKO Bexarotene / C57BL/6 LXRdKO mouse liver / . +2135 GSM864677 /home/drk/tillage/datasets/mouse/chip/geo/GSM864677/summary/coverage.w5 256 64 1.0 sum 2135 CHIP:RXR:LXRdKO Control / C57BL/6 LXRdKO mouse liver / . +2136 GSM864678 /home/drk/tillage/datasets/mouse/chip/geo/GSM864678/summary/coverage.w5 256 64 1.0 sum 2136 CHIP:RXR:LXRdKO T0901317 / C57BL/6 LXRdKO mouse liver / . +2137 GSM864679 /home/drk/tillage/datasets/mouse/chip/geo/GSM864679/summary/coverage.w5 256 64 1.0 sum 2137 CHIP:PolII:WT Control replicate 1 / C57BL/6 wild type mouse liver / . +2138 GSM864681 /home/drk/tillage/datasets/mouse/chip/geo/GSM864681/summary/coverage.w5 256 64 1.0 sum 2138 CHIP:PolII:WT Bexarotene replicate 1 / C57BL/6 wild type mouse liver / . +2139 GSM864683 /home/drk/tillage/datasets/mouse/chip/geo/GSM864683/summary/coverage.w5 256 64 1.0 sum 2139 CHIP:PolII:WT T0901317 replicate 1 / C57BL/6 wild type mouse liver / . +2140 GSM864685 /home/drk/tillage/datasets/mouse/chip/geo/GSM864685/summary/coverage.w5 256 64 1.0 sum 2140 CHIP:PolII:LXRdKO Control replicate 1 / C57BL/6 LXRdKO mouse liver / . +2141 GSM864687 /home/drk/tillage/datasets/mouse/chip/geo/GSM864687/summary/coverage.w5 256 64 1.0 sum 2141 CHIP:PolII:LXRdKO Bexarotene replicate 1 / C57BL/6 LXRdKO mouse liver / . +2142 GSM864689 /home/drk/tillage/datasets/mouse/chip/geo/GSM864689/summary/coverage.w5 256 64 1.0 sum 2142 CHIP:PolII:LXRdKO T0901317 replicate 1 / C57BL/6 LXRdKO mouse liver / . +2143 GSM873424 /home/drk/tillage/datasets/mouse/chip/geo/GSM873424/summary/coverage.w5 256 64 1.0 sum 2143 CHIP:CHOP:Chop+/+ Tm ChIP-seq / Mouse embronic fibroblast / Mouse embryonic fibroblast +2144 GSM873425 /home/drk/tillage/datasets/mouse/chip/geo/GSM873425/summary/coverage.w5 256 64 1.0 sum 2144 CHIP:CHOP:Chop -/- Tm ChIP-seq / Mouse embronic fibroblast / Mouse embryonic fibroblast +2145 GSM873426 /home/drk/tillage/datasets/mouse/chip/geo/GSM873426/summary/coverage.w5 256 64 1.0 sum 2145 CHIP:ATF4:Atf4+/+ Tm ChIP-seq / Mouse embronic fibroblast / Mouse embryonic fibroblast +2146 GSM873427 /home/drk/tillage/datasets/mouse/chip/geo/GSM873427/summary/coverage.w5 256 64 1.0 sum 2146 CHIP:ATF4:Atf4-/ Tm ChIP-seq / Mouse embronic fibroblast / Mouse embryonic fibroblast +2147 GSM874950 /home/drk/tillage/datasets/mouse/chip/geo/GSM874950/summary/coverage.w5 256 64 1.0 sum 2147 CHIP:RPB2:Polr2b_ZT02 / RPB2 IP / . +2148 GSM874951 /home/drk/tillage/datasets/mouse/chip/geo/GSM874951/summary/coverage.w5 256 64 1.0 sum 2148 CHIP:RPB2:Polr2b_ZT06 / RPB2 IP / . +2149 GSM874952 /home/drk/tillage/datasets/mouse/chip/geo/GSM874952/summary/coverage.w5 256 64 1.0 sum 2149 CHIP:RPB2:Polr2b_ZT10 / RPB2 IP / . +2150 GSM874953 /home/drk/tillage/datasets/mouse/chip/geo/GSM874953/summary/coverage.w5 256 64 1.0 sum 2150 CHIP:RPB2:Polr2b_ZT14 / RPB2 IP / . +2151 GSM874954 /home/drk/tillage/datasets/mouse/chip/geo/GSM874954/summary/coverage.w5 256 64 1.0 sum 2151 CHIP:RPB2:Polr2b_ZT18 / RPB2 IP / . +2152 GSM874955 /home/drk/tillage/datasets/mouse/chip/geo/GSM874955/summary/coverage.w5 256 64 1.0 sum 2152 CHIP:RPB2:Polr2b_ZT22 / RPB2 IP / . +2153 GSM874956 /home/drk/tillage/datasets/mouse/chip/geo/GSM874956/summary/coverage.w5 256 64 1.0 sum 2153 CHIP:RPB2:Polr2b_ZT26 / RPB2 IP / . +2154 GSM874957 /home/drk/tillage/datasets/mouse/chip/geo/GSM874957/summary/coverage.w5 256 64 1.0 sum 2154 CHIP:H3K4me3:H3K4me3_ZT02 / H3K4me3 IP / . +2155 GSM874958 /home/drk/tillage/datasets/mouse/chip/geo/GSM874958/summary/coverage.w5 256 64 1.0 sum 2155 CHIP:H3K4me3:H3K4me3_ZT06 / H3K4me3 IP / . +2156 GSM874959 /home/drk/tillage/datasets/mouse/chip/geo/GSM874959/summary/coverage.w5 256 64 1.0 sum 2156 CHIP:H3K4me3:H3K4me3_ZT10 / H3K4me3 IP / . +2157 GSM874960 /home/drk/tillage/datasets/mouse/chip/geo/GSM874960/summary/coverage.w5 256 64 1.0 sum 2157 CHIP:H3K4me3:H3K4me3_ZT14 / H3K4me3 IP / . +2158 GSM874961 /home/drk/tillage/datasets/mouse/chip/geo/GSM874961/summary/coverage.w5 256 64 1.0 sum 2158 CHIP:H3K4me3:H3K4me3_ZT18 / H3K4me3 IP / . +2159 GSM874962 /home/drk/tillage/datasets/mouse/chip/geo/GSM874962/summary/coverage.w5 256 64 1.0 sum 2159 CHIP:H3K4me3:H3K4me3_ZT22 / H3K4me3 IP / . +2160 GSM874963 /home/drk/tillage/datasets/mouse/chip/geo/GSM874963/summary/coverage.w5 256 64 1.0 sum 2160 CHIP:H3K4me3:H3K4me3_ZT26 / H3K4me3 IP / . +2161 GSM874964 /home/drk/tillage/datasets/mouse/chip/geo/GSM874964/summary/coverage.w5 256 64 1.0 sum 2161 CHIP:H3K36me3:H3K36me3_ZT02 / H3K36me3 IP / . +2162 GSM874965 /home/drk/tillage/datasets/mouse/chip/geo/GSM874965/summary/coverage.w5 256 64 1.0 sum 2162 CHIP:H3K36me3:H3K36me3_ZT06 / H3K36me3 IP / . +2163 GSM874966 /home/drk/tillage/datasets/mouse/chip/geo/GSM874966/summary/coverage.w5 256 64 1.0 sum 2163 CHIP:H3K36me3:H3K36me3_ZT10 / H3K36me3 IP / . +2164 GSM874967 /home/drk/tillage/datasets/mouse/chip/geo/GSM874967/summary/coverage.w5 256 64 1.0 sum 2164 CHIP:H3K36me3:H3K36me3_ZT14 / H3K36me3 IP / . +2165 GSM874968 /home/drk/tillage/datasets/mouse/chip/geo/GSM874968/summary/coverage.w5 256 64 1.0 sum 2165 CHIP:H3K36me3:H3K36me3_ZT18 / H3K36me3 IP / . +2166 GSM874969 /home/drk/tillage/datasets/mouse/chip/geo/GSM874969/summary/coverage.w5 256 64 1.0 sum 2166 CHIP:H3K36me3:H3K36me3_ZT22 / H3K36me3 IP / . +2167 GSM874970 /home/drk/tillage/datasets/mouse/chip/geo/GSM874970/summary/coverage.w5 256 64 1.0 sum 2167 CHIP:H3K36me3:H3K36me3_ZT26 / H3K36me3 IP / . +2168 ENCFF130ROA /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AHX/summary/coverage.w5 768 384 0.3 sum_sqrt 2168 RNA:C3H10T1/2 +2169 ENCFF641HYO /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AHY/summary/coverage.w5 768 384 0.3 sum_sqrt 2169 RNA:C2C12 +2170 ENCFF018XGZ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AHZ/summary/coverage.w5 768 384 0.3 sum_sqrt 2170 RNA:C3H10T1/2 +2171 ENCFF777WNL /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AIA/summary/coverage.w5 768 384 0.3 sum_sqrt 2171 RNA:myocyte originated from C2C12 +2172 ENCFF798FMB+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AJU/summary/coverage+.w5 768 384 0.3 sum_sqrt 2173 RNA:C57BL/6J liver tissue adult (8 weeks) +2173 ENCFF798FMB- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AJU/summary/coverage-.w5 768 384 0.3 sum_sqrt 2172 RNA:C57BL/6J liver tissue adult (8 weeks) +2174 ENCFF419YHB+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AJV/summary/coverage+.w5 768 384 0.3 sum_sqrt 2175 RNA:B10.H-2aH-4bp/Wts CH12.LX +2175 ENCFF419YHB- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000AJV/summary/coverage-.w5 768 384 0.3 sum_sqrt 2174 RNA:B10.H-2aH-4bp/Wts CH12.LX +2176 ENCFF085QPW+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYP/summary/coverage+.w5 768 384 0.3 sum_sqrt 2177 RNA:C57BL/6J colon tissue adult (8 weeks) +2177 ENCFF085QPW- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYP/summary/coverage-.w5 768 384 0.3 sum_sqrt 2176 RNA:C57BL/6J colon tissue adult (8 weeks) +2178 ENCFF558JWN+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 2179 RNA:C57BL/6J heart tissue adult (8 weeks) +2179 ENCFF558JWN- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 2178 RNA:C57BL/6J heart tissue adult (8 weeks) +2180 ENCFF878WGQ+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYR/summary/coverage+.w5 768 384 0.3 sum_sqrt 2181 RNA:C57BL/6J kidney tissue adult (8 weeks) +2181 ENCFF878WGQ- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYR/summary/coverage-.w5 768 384 0.3 sum_sqrt 2180 RNA:C57BL/6J kidney tissue adult (8 weeks) +2182 ENCFF995EIJ+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYS/summary/coverage+.w5 768 384 0.3 sum_sqrt 2183 RNA:C57BL/6J liver tissue adult (8 weeks) +2183 ENCFF995EIJ- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYS/summary/coverage-.w5 768 384 0.3 sum_sqrt 2182 RNA:C57BL/6J liver tissue adult (8 weeks) +2184 ENCFF070OKD+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYT/summary/coverage+.w5 768 384 0.3 sum_sqrt 2185 RNA:C57BL/6J lung tissue adult (8 weeks) +2185 ENCFF070OKD- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYT/summary/coverage-.w5 768 384 0.3 sum_sqrt 2184 RNA:C57BL/6J lung tissue adult (8 weeks) +2186 ENCFF828PDL+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYU/summary/coverage+.w5 768 384 0.3 sum_sqrt 2187 RNA:C57BL/6J spleen tissue adult (8 weeks) +2187 ENCFF828PDL- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYU/summary/coverage-.w5 768 384 0.3 sum_sqrt 2186 RNA:C57BL/6J spleen tissue adult (8 weeks) +2188 ENCFF978UIY+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYV/summary/coverage+.w5 768 384 0.3 sum_sqrt 2189 RNA:C57BL/6J thymus tissue adult (8 weeks) +2189 ENCFF978UIY- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYV/summary/coverage-.w5 768 384 0.3 sum_sqrt 2188 RNA:C57BL/6J thymus tissue adult (8 weeks) +2190 ENCFF216HBX+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYW/summary/coverage+.w5 768 384 0.3 sum_sqrt 2191 RNA:C57BL/6J testis tissue male adult (8 weeks) +2191 ENCFF216HBX- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYW/summary/coverage-.w5 768 384 0.3 sum_sqrt 2190 RNA:C57BL/6J testis tissue male adult (8 weeks) +2192 ENCFF341NKU+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYX/summary/coverage+.w5 768 384 0.3 sum_sqrt 2193 RNA:C57BL/6J adrenal gland tissue adult (8 weeks) +2193 ENCFF341NKU- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYX/summary/coverage-.w5 768 384 0.3 sum_sqrt 2192 RNA:C57BL/6J adrenal gland tissue adult (8 weeks) +2194 ENCFF721GSY+ /home/drk/tillage/datasets/mouse/rna/encode/ENCSR000BYY/summary/coverage+.w5 768 384 0.3 sum_sqrt 2195 RNA:C57BL/6J duodenum tissue adult (8 weeks) 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/home/drk/tillage/datasets/mouse/rna/encode/ENCSR996TVY/summary/coverage+.w5 768 384 0.3 sum_sqrt 2607 RNA:B6CASTF1/J left cerebral cortex tissue male adult (18-20 months) +2607 ENCFF422YPA- /home/drk/tillage/datasets/mouse/rna/encode/ENCSR996TVY/summary/coverage-.w5 768 384 0.3 sum_sqrt 2606 RNA:B6CASTF1/J left cerebral cortex tissue male adult (18-20 months) diff --git a/examples/targets_rna.txt b/examples/targets_rna.txt new file mode 100644 index 0000000..29c7f27 --- /dev/null +++ b/examples/targets_rna.txt @@ -0,0 +1,1544 @@ + identifier file clip clip_soft scale sum_stat strand_pair description +6068 ENCFF281BWX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6069 RNA:aortic smooth muscle cell male adult (21 years) and male adult (54 years) +6069 ENCFF281BWX- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6068 RNA:aortic smooth muscle cell male adult (21 years) and male adult (54 years) +6070 ENCFF168OLY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAB/summary/coverage+.w5 768 384 0.3 sum_sqrt 6071 RNA:bladder microvascular endothelial cell male adult (46 years) and male adult (60 years) +6071 ENCFF168OLY- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAB/summary/coverage-.w5 768 384 0.3 sum_sqrt 6070 RNA:bladder microvascular endothelial cell male adult (46 years) and male adult (60 years) +6072 ENCFF442VHH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6073 RNA:smooth muscle cell of bladder female adult (53 years) and male adult (62 years) +6073 ENCFF442VHH- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6072 RNA:smooth muscle cell of bladder female adult (53 years) and male adult (62 years) +6074 ENCFF153YEN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6075 RNA:bronchial epithelial cell female adult (40 years) and male adult (68 years) +6075 ENCFF153YEN- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6074 RNA:bronchial epithelial cell female adult (40 years) and male adult (68 years) +6076 ENCFF383NTW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6077 RNA:bronchial smooth muscle cell male adult (52 years) and male adult (59 years) +6077 ENCFF383NTW- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6076 RNA:bronchial smooth muscle cell male adult (52 years) and male adult (59 years) +6078 ENCFF226UWU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6079 RNA:endothelial cell of coronary artery female adult (41 years) and male adult (77 years) +6079 ENCFF226UWU- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6078 RNA:endothelial cell of coronary artery female adult (41 years) and male adult (77 years) +6080 ENCFF537AIY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6081 RNA:smooth muscle cell of the coronary artery female adult (53 years) and male adult (55 years) +6081 ENCFF537AIY- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6080 RNA:smooth muscle cell of the coronary artery female adult (53 years) and male adult (55 years) +6082 ENCFF263MKB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6083 RNA:regular cardiac myocyte female adult (51 years) and male adult (48 years) +6083 ENCFF263MKB- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6082 RNA:regular cardiac myocyte female adult (51 years) and male adult (48 years) +6084 ENCFF366CCB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAI/summary/coverage+.w5 768 384 0.3 sum_sqrt 6085 RNA:dermis blood vessel endothelial cell female child (16 years) and male child (13 years) +6085 ENCFF366CCB- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6084 RNA:dermis blood vessel endothelial cell female child (16 years) and male child (13 years) +6086 ENCFF805UDX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6087 RNA:dermis lymphatic vessel endothelial cell female adult (45 years) and male child (6 years) +6087 ENCFF805UDX- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6086 RNA:dermis lymphatic vessel endothelial cell female adult (45 years) and male child (6 years) +6088 ENCFF079OMS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6089 RNA:dermis microvascular lymphatic vessel endothelial cell female adult (38 years) and female adult (64 years) +6089 ENCFF079OMS- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6088 RNA:dermis microvascular lymphatic vessel endothelial cell female adult (38 years) and female adult (64 years) +6090 ENCFF114NWW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6091 RNA:nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa female adult (70 years) and male adult (46 years) +6091 ENCFF114NWW- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6090 RNA:nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa female adult (70 years) and male adult (46 years) +6092 ENCFF520FAO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6093 RNA:pulmonary artery endothelial cell male adult (23 years) and male adult (52 years) +6093 ENCFF520FAO- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6092 RNA:pulmonary artery endothelial cell male adult (23 years) and male adult (52 years) +6094 ENCFF679XSO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6095 RNA:smooth muscle cell of the pulmonary artery male adult (26 years) and male adult (28 years) +6095 ENCFF679XSO- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6094 RNA:smooth muscle cell of the pulmonary artery male adult (26 years) and male adult (28 years) +6096 ENCFF556PAF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6097 RNA:fibroblast of lung female adult (83 years) and male adult (23 years) +6097 ENCFF556PAF- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6096 RNA:fibroblast of lung female adult (83 years) and male adult (23 years) +6098 ENCFF618FQK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6099 RNA:lung microvascular endothelial cell female adult (55 years) and male adult (63 years) +6099 ENCFF618FQK- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6098 RNA:lung microvascular endothelial cell female adult (55 years) and male adult (63 years) +6100 ENCFF818OXF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6101 RNA:renal cortical epithelial cell female adult (69 years) and male adult (84 years) +6101 ENCFF818OXF- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6100 RNA:renal cortical epithelial cell female adult (69 years) and male adult (84 years) +6102 ENCFF520NFI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6103 RNA:tracheal epithelial cell male adult (21 years) and male adult (68 years) +6103 ENCFF520NFI- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6102 RNA:tracheal epithelial cell male adult (21 years) and male adult (68 years) +6104 ENCFF749ZJH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6105 RNA:smooth muscle cell of trachea male adult (28 years) and male adult (56 years) +6105 ENCFF749ZJH- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6104 RNA:smooth muscle cell of trachea male adult (28 years) and male adult (56 years) +6106 ENCFF572FWT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6107 RNA:epithelial cell of umbilical artery female newborn and male newborn +6107 ENCFF572FWT- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6106 RNA:epithelial cell of umbilical artery female newborn and male newborn +6108 ENCFF096HEZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6109 RNA:smooth muscle cell of the umbilical artery female newborn and male newborn +6109 ENCFF096HEZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6108 RNA:smooth muscle cell of the umbilical artery female newborn and male newborn +6110 ENCFF360EXL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAV/summary/coverage+.w5 768 384 0.3 sum_sqrt 6111 RNA:uterine smooth muscle cell female adult (48 years) and female adult (50 years) +6111 ENCFF360EXL- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AAV/summary/coverage-.w5 768 384 0.3 sum_sqrt 6110 RNA:uterine smooth muscle cell female adult (48 years) and female adult (50 years) +6112 ENCFF470BSF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6113 RNA:GM12878 +6113 ENCFF470BSF- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6112 RNA:GM12878 +6114 ENCFF617ZDV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AED/summary/coverage+.w5 768 384 0.3 sum_sqrt 6115 RNA:GM12878 +6115 ENCFF617ZDV- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AED/summary/coverage-.w5 768 384 0.3 sum_sqrt 6114 RNA:GM12878 +6116 ENCFF993POP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6117 RNA:GM12878 +6117 ENCFF993POP- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6116 RNA:GM12878 +6118 ENCFF678ITA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6119 RNA:GM12878 +6119 ENCFF678ITA- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6118 RNA:GM12878 +6120 ENCFF812WIL /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEG/summary/coverage.w5 768 384 0.3 sum_sqrt 6120 RNA:GM12878 +6121 ENCFF142WGV /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEH/summary/coverage.w5 768 384 0.3 sum_sqrt 6121 RNA:GM12878 +6122 ENCFF980ZHM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6123 RNA:K562 +6123 ENCFF980ZHM- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6122 RNA:K562 +6124 ENCFF132DVY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6125 RNA:K562 +6125 ENCFF132DVY- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6124 RNA:K562 +6126 ENCFF919EXM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6127 RNA:K562 +6127 ENCFF919EXM- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6126 RNA:K562 +6128 ENCFF552CYS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6129 RNA:K562 +6129 ENCFF552CYS- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6128 RNA:K562 +6130 ENCFF991BRF /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEP/summary/coverage.w5 768 384 0.3 sum_sqrt 6130 RNA:K562 +6131 ENCFF769VLM /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6131 RNA:K562 +6132 ENCFF945UHI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6133 RNA:liver tissue female child (6 years) and with nonobstructive coronary artery disease; liver tissue male adult (32 years) +6133 ENCFF945UHI- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6132 RNA:liver tissue female child (6 years) and with nonobstructive coronary artery disease; liver tissue male adult (32 years) +6134 ENCFF775XPO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEV/summary/coverage+.w5 768 384 0.3 sum_sqrt 6135 RNA:urinary bladder tissue female embryo (20 weeks) and female embryo (24 weeks) +6135 ENCFF775XPO- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEV/summary/coverage-.w5 768 384 0.3 sum_sqrt 6134 RNA:urinary bladder tissue female embryo (20 weeks) and female embryo (24 weeks) +6136 ENCFF638TDD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6137 RNA:cerebellum tissue female embryo (19 weeks) and female embryo (37 weeks) +6137 ENCFF638TDD- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6136 RNA:cerebellum tissue female embryo (19 weeks) and female embryo (37 weeks) +6138 ENCFF355IUO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEX/summary/coverage+.w5 768 384 0.3 sum_sqrt 6139 RNA:diencephalon tissue female embryo (20 weeks) and male embryo (22 weeks) +6139 ENCFF355IUO- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEX/summary/coverage-.w5 768 384 0.3 sum_sqrt 6138 RNA:diencephalon tissue female embryo (20 weeks) and male embryo (22 weeks) +6140 ENCFF217HQN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEY/summary/coverage+.w5 768 384 0.3 sum_sqrt 6141 RNA:frontal cortex tissue female embryo (20 weeks) and male embryo (22 weeks) +6141 ENCFF217HQN- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEY/summary/coverage-.w5 768 384 0.3 sum_sqrt 6140 RNA:frontal cortex tissue female embryo (20 weeks) and male embryo (22 weeks) +6142 ENCFF454SXU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6143 RNA:heart tissue female embryo (19 weeks) and female embryo (28 weeks) +6143 ENCFF454SXU- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AEZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6142 RNA:heart tissue female embryo (19 weeks) and female embryo (28 weeks) +6144 ENCFF367PUX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6145 RNA:metanephros tissue female embryo (20 weeks) and female embryo (24 weeks) +6145 ENCFF367PUX- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6144 RNA:metanephros tissue female embryo (20 weeks) and female embryo (24 weeks) +6146 ENCFF630VID+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFB/summary/coverage+.w5 768 384 0.3 sum_sqrt 6147 RNA:liver tissue female embryo (20 weeks) and male embryo (22 weeks) +6147 ENCFF630VID- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFB/summary/coverage-.w5 768 384 0.3 sum_sqrt 6146 RNA:liver tissue female embryo (20 weeks) and male embryo (22 weeks) +6148 ENCFF892OBT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6149 RNA:lung tissue female embryo (20 weeks) and female embryo (24 weeks) +6149 ENCFF892OBT- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6148 RNA:lung tissue female embryo (20 weeks) and female embryo (24 weeks) +6150 ENCFF537TSF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6151 RNA:occipital lobe tissue female embryo (20 weeks) and male embryo (22 weeks) +6151 ENCFF537TSF- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6150 RNA:occipital lobe tissue female embryo (20 weeks) and male embryo (22 weeks) +6152 ENCFF470OAY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6153 RNA:parietal lobe tissue female embryo (24 weeks) and male embryo (22 weeks) +6153 ENCFF470OAY- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6152 RNA:parietal lobe tissue female embryo (24 weeks) and male embryo (22 weeks) +6154 ENCFF285OHV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6155 RNA:skeletal muscle tissue tissue female embryo (19 weeks) and male embryo (22 weeks) +6155 ENCFF285OHV- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6154 RNA:skeletal muscle tissue tissue female embryo (19 weeks) and male embryo (22 weeks) +6156 ENCFF198TLM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6157 RNA:skin of body tissue female embryo (24 weeks) and male embryo (22 weeks) +6157 ENCFF198TLM- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6156 RNA:skin of body tissue female embryo (24 weeks) and male embryo (22 weeks) +6158 ENCFF768YRQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6159 RNA:spinal cord tissue female embryo (24 weeks) and male embryo (22 weeks) +6159 ENCFF768YRQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6158 RNA:spinal cord tissue female embryo (24 weeks) and male embryo (22 weeks) +6160 ENCFF718MVN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFI/summary/coverage+.w5 768 384 0.3 sum_sqrt 6161 RNA:stomach tissue female embryo (40 weeks) and male embryo (36 weeks) +6161 ENCFF718MVN- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6160 RNA:stomach tissue female embryo (40 weeks) and male embryo (36 weeks) +6162 ENCFF709SZT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6163 RNA:temporal lobe tissue female embryo (20 weeks) and female embryo (24 weeks) +6163 ENCFF709SZT- /home/drk/tillage/datasets/human/rna/encode/ENCSR000AFJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6162 RNA:temporal lobe tissue female embryo (20 weeks) and female embryo (24 weeks) +6164 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768 384 0.3 sum_sqrt 6277 RNA:SK-N-SH nuclear fraction +6277 ENCFF256CAM- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6276 RNA:SK-N-SH nuclear fraction +6278 ENCFF601EJS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6279 RNA:SK-N-SH +6279 ENCFF601EJS- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6278 RNA:SK-N-SH +6280 ENCFF297JKU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6281 RNA:MCF-7 cytosolic fraction +6281 ENCFF297JKU- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6280 RNA:MCF-7 cytosolic fraction +6282 ENCFF252DFZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTV/summary/coverage+.w5 768 384 0.3 sum_sqrt 6283 RNA:B cell female adult (27 years) and female adult (43 years) +6283 ENCFF252DFZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTV/summary/coverage-.w5 768 384 0.3 sum_sqrt 6282 RNA:B cell female adult (27 years) and female adult (43 years) +6284 ENCFF779FMR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTX/summary/coverage+.w5 768 384 0.3 sum_sqrt 6285 RNA:placental pericyte female newborn and male newborn +6285 ENCFF779FMR- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTX/summary/coverage-.w5 768 384 0.3 sum_sqrt 6284 RNA:placental pericyte female newborn and male newborn +6286 ENCFF653TAB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6287 RNA:mesenchymal stem cell of adipose female adult (37 years) and female adult (42 years) +6287 ENCFF653TAB- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CTZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6286 RNA:mesenchymal stem cell of adipose female adult (37 years) and female adult (42 years) +6288 ENCFF841GMC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6289 RNA:hematopoietic multipotent progenitor cell +6289 ENCFF841GMC- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6288 RNA:hematopoietic multipotent progenitor cell +6290 ENCFF798NEI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUB/summary/coverage+.w5 768 384 0.3 sum_sqrt 6291 RNA:hair follicle dermal papilla cell female adult (47 years) and female adult (70 years) +6291 ENCFF798NEI- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUB/summary/coverage-.w5 768 384 0.3 sum_sqrt 6290 RNA:hair follicle dermal papilla cell female adult (47 years) and female adult (70 years) +6292 ENCFF023YXV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6293 RNA:CD14-positive monocyte female +6293 ENCFF023YXV- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6292 RNA:CD14-positive monocyte female +6294 ENCFF359MTP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6295 RNA:mesenchymal stem cell of the bone marrow female adult (60 years) and male adult (57 years) +6295 ENCFF359MTP- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6294 RNA:mesenchymal stem cell of the bone marrow female adult (60 years) and male adult (57 years) +6296 ENCFF314QIG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6297 RNA:articular chondrocyte of knee joint female adult (56 years) and male adult (64 years) +6297 ENCFF314QIG- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6296 RNA:articular chondrocyte of knee joint female adult (56 years) and male adult (64 years) +6298 ENCFF953CRN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6299 RNA:osteoblast female adult (56 years) and male adult (62 years) +6299 ENCFF953CRN- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6298 RNA:osteoblast female adult (56 years) and male adult (62 years) +6300 ENCFF143TXA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6301 RNA:vein endothelial cell male adult (48 years) and male adult (52 years) +6301 ENCFF143TXA- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6300 RNA:vein endothelial cell male adult (48 years) and male adult (52 years) +6302 ENCFF343FWG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6303 RNA:fibroblast of dermis female adult (44 years) and female adult (55 years) +6303 ENCFF343FWG- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6302 RNA:fibroblast of dermis female adult (44 years) and female adult (55 years) +6304 ENCFF804YRV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUI/summary/coverage+.w5 768 384 0.3 sum_sqrt 6305 RNA:skeletal muscle satellite cell female adult (64 years) and male adult (21 years) +6305 ENCFF804YRV- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6304 RNA:skeletal muscle satellite cell female adult (64 years) and male adult (21 years) +6306 ENCFF256ZZS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6307 RNA:fibroblast of the aortic adventitia female adult (24 years) and male adult (47 years) +6307 ENCFF256ZZS- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6306 RNA:fibroblast of the aortic adventitia female adult (24 years) and male adult (47 years) +6308 ENCFF805HMR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6309 RNA:thoracic aorta endothelial cell female adult (22 years) and male adult (55 years) +6309 ENCFF805HMR- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6308 RNA:thoracic aorta endothelial cell female adult (22 years) and male adult (55 years) +6310 ENCFF649CUP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6311 RNA:fibroblast of villous mesenchyme female newborn and male newborn +6311 ENCFF649CUP- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6310 RNA:fibroblast of villous mesenchyme female newborn and male newborn +6312 ENCFF233TOO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6313 RNA:subcutaneous preadipocyte female adult (62 years) and male adult (65 years) +6313 ENCFF233TOO- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6312 RNA:subcutaneous preadipocyte female adult (62 years) and male adult (65 years) +6314 ENCFF096YBH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6315 RNA:mammary epithelial cell female adult (23 years) +6315 ENCFF096YBH- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6314 RNA:mammary epithelial cell female adult (23 years) +6316 ENCFF492ICA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6317 RNA:mesenchymal stem cell of Wharton's jelly female newborn and male newborn +6317 ENCFF492ICA- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6316 RNA:mesenchymal stem cell of Wharton's jelly female newborn and male newborn +6318 ENCFF591NKN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6319 RNA:placental epithelial cell female newborn and male newborn +6319 ENCFF591NKN- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6318 RNA:placental epithelial cell female newborn and male newborn +6320 ENCFF723WDG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6321 RNA:melanocyte of skin male child (1 year) and male child (3 years) +6321 ENCFF723WDG- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6320 RNA:melanocyte of skin male child (1 year) and male child (3 years) +6322 ENCFF230ZSG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6323 RNA:melanocyte of skin female adult (52 years) and male adult (55 years) +6323 ENCFF230ZSG- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6322 RNA:melanocyte of skin female adult (52 years) and male adult (55 years) +6324 ENCFF151XTV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6325 RNA:mononuclear cell female adult (52 years) +6325 ENCFF151XTV- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CUT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6324 RNA:mononuclear cell female adult (52 years) +6326 ENCFF853JVS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CVT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6327 RNA:GM12878 nucleolus fraction +6327 ENCFF853JVS- /home/drk/tillage/datasets/human/rna/encode/ENCSR000CVT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6326 RNA:GM12878 nucleolus fraction +6328 ENCFF982YRZ /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWG/summary/coverage.w5 768 384 0.3 sum_sqrt 6328 RNA:K562 treated with Interferon gamma for 6 hours +6329 ENCFF594PZM /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWH/summary/coverage.w5 768 384 0.3 sum_sqrt 6329 RNA:K562 treated with Interferon gamma for 30 minutes +6330 ENCFF722OTS /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWI/summary/coverage.w5 768 384 0.3 sum_sqrt 6330 RNA:K562 treated with interferon alpha for 6 hours +6331 ENCFF311UQI /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWJ/summary/coverage.w5 768 384 0.3 sum_sqrt 6331 RNA:K562 treated with interferon alpha for 30 minutes +6332 ENCFF987SCM /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWK/summary/coverage.w5 768 384 0.3 sum_sqrt 6332 RNA:GM12891 +6333 ENCFF659BXA /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWL/summary/coverage.w5 768 384 0.3 sum_sqrt 6333 RNA:GM12892 +6334 ENCFF069PST /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWM/summary/coverage.w5 768 384 0.3 sum_sqrt 6334 RNA:HCT116 +6335 ENCFF106FBY /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWN/summary/coverage.w5 768 384 0.3 sum_sqrt 6335 RNA:skeletal muscle myoblast +6336 ENCFF543YFY /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWO/summary/coverage.w5 768 384 0.3 sum_sqrt 6336 RNA:myocyte originated from LHCN-M2 +6337 ENCFF905ISC /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWP/summary/coverage.w5 768 384 0.3 sum_sqrt 6337 RNA:LHCN-M2 +6338 ENCFF808PHI /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6338 RNA:MCF-7 +6339 ENCFF036JNR /home/drk/tillage/datasets/human/rna/encode/ENCSR000CWR/summary/coverage.w5 768 384 0.3 sum_sqrt 6339 RNA:fibroblast of lung +6340 ENCFF684NXV /home/drk/tillage/datasets/human/rna/encode/ENCSR000EYN/summary/coverage.w5 768 384 0.3 sum_sqrt 6340 RNA:GM12878 +6341 ENCFF860AKE /home/drk/tillage/datasets/human/rna/encode/ENCSR000EYO/summary/coverage.w5 768 384 0.3 sum_sqrt 6341 RNA:K562 +6342 ENCFF687EZU /home/drk/tillage/datasets/human/rna/encode/ENCSR000EYP/summary/coverage.w5 768 384 0.3 sum_sqrt 6342 RNA:H1 +6343 ENCFF587FSZ /home/drk/tillage/datasets/human/rna/encode/ENCSR000EYQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6343 RNA:HeLa-S3 +6344 ENCFF995HXY /home/drk/tillage/datasets/human/rna/encode/ENCSR000EYR/summary/coverage.w5 768 384 0.3 sum_sqrt 6344 RNA:HepG2 +6345 ENCFF618GYZ /home/drk/tillage/datasets/human/rna/encode/ENCSR000EYS/summary/coverage.w5 768 384 0.3 sum_sqrt 6345 RNA:endothelial cell of umbilical vein newborn +6346 ENCFF609GRY /home/drk/tillage/datasets/human/rna/encode/ENCSR000EYT/summary/coverage.w5 768 384 0.3 sum_sqrt 6346 RNA:keratinocyte female +6347 ENCFF155OWV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR001HHK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6348 RNA:OCI-LY7 +6348 ENCFF155OWV- /home/drk/tillage/datasets/human/rna/encode/ENCSR001HHK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6347 RNA:OCI-LY7 +6349 ENCFF227YIR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR001UXR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6350 RNA:pancreas tissue female adult (30 years) +6350 ENCFF227YIR- /home/drk/tillage/datasets/human/rna/encode/ENCSR001UXR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6349 RNA:pancreas tissue female adult (30 years) +6351 ENCFF775NPV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR002CTR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6352 RNA:endodermal cell originated from HUES64 +6352 ENCFF775NPV- /home/drk/tillage/datasets/human/rna/encode/ENCSR002CTR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6351 RNA:endodermal cell originated from HUES64 +6353 ENCFF357VZF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR003BTD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6354 RNA:adrenal gland tissue female adult (47 years) +6354 ENCFF357VZF- /home/drk/tillage/datasets/human/rna/encode/ENCSR003BTD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6353 RNA:adrenal gland tissue female adult (47 years) +6355 ENCFF496WON /home/drk/tillage/datasets/human/rna/encode/ENCSR006EBD/summary/coverage.w5 768 384 0.3 sum_sqrt 6355 RNA:K562 treated with 100 nM GSK J4 for 4 hours +6356 ENCFF028ZKC /home/drk/tillage/datasets/human/rna/encode/ENCSR007OKF/summary/coverage.w5 768 384 0.3 sum_sqrt 6356 RNA:CD8-positive, alpha-beta memory T cell +6357 ENCFF719AYC /home/drk/tillage/datasets/human/rna/encode/ENCSR015EMF/summary/coverage.w5 768 384 0.3 sum_sqrt 6357 RNA:left renal cortex interstitium tissue male embryo (105 days) +6358 ENCFF952CKD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR015PUN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6359 RNA:Right ventricle myocardium inferior tissue male adult (60 years) +6359 ENCFF952CKD- /home/drk/tillage/datasets/human/rna/encode/ENCSR015PUN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6358 RNA:Right ventricle myocardium inferior tissue male adult (60 years) +6360 ENCFF233HJC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR019ICB/summary/coverage+.w5 768 384 0.3 sum_sqrt 6361 RNA:middle frontal area 46 tissue female adult (90 or above years) +6361 ENCFF233HJC- /home/drk/tillage/datasets/human/rna/encode/ENCSR019ICB/summary/coverage-.w5 768 384 0.3 sum_sqrt 6360 RNA:middle frontal area 46 tissue female adult (90 or above years) +6362 ENCFF626VIR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR019MXZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6363 RNA:HepG2 insoluble cytoplasmic fraction +6363 ENCFF626VIR- /home/drk/tillage/datasets/human/rna/encode/ENCSR019MXZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6362 RNA:HepG2 insoluble cytoplasmic fraction +6364 ENCFF401YXF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR020YQE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6365 RNA:mammary epithelial cell female +6365 ENCFF401YXF- /home/drk/tillage/datasets/human/rna/encode/ENCSR020YQE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6364 RNA:mammary epithelial cell female +6366 ENCFF354WKE /home/drk/tillage/datasets/human/rna/encode/ENCSR022MON/summary/coverage.w5 768 384 0.3 sum_sqrt 6366 RNA:fibroblast of skin of scalp male embryo (97 days) +6367 ENCFF044XSJ /home/drk/tillage/datasets/human/rna/encode/ENCSR023VVO/summary/coverage.w5 768 384 0.3 sum_sqrt 6367 RNA:bipolar neuron originated from GM23338 treated with 0.5 ug/mL doxycycline hyclate for 4 days +6368 ENCFF796PND+ /home/drk/tillage/datasets/human/rna/encode/ENCSR023ZXN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6369 RNA:thyroid gland tissue male adult (54 years) +6369 ENCFF796PND- /home/drk/tillage/datasets/human/rna/encode/ENCSR023ZXN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6368 RNA:thyroid gland tissue male adult (54 years) +6370 ENCFF408WKS /home/drk/tillage/datasets/human/rna/encode/ENCSR027EJD/summary/coverage.w5 768 384 0.3 sum_sqrt 6370 RNA:muscle of back tissue female embryo (115 days) +6371 ENCFF123MLK /home/drk/tillage/datasets/human/rna/encode/ENCSR029FTY/summary/coverage.w5 768 384 0.3 sum_sqrt 6371 RNA:left renal pelvis tissue male embryo (105 days) +6372 ENCFF182JIC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR029KNZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6373 RNA:testis tissue male adult (37 years) +6373 ENCFF182JIC- /home/drk/tillage/datasets/human/rna/encode/ENCSR029KNZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6372 RNA:testis tissue male adult (37 years) +6374 ENCFF579IBH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR033XWU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6375 RNA:CD4-positive, alpha-beta T cell male adult (20 years) +6375 ENCFF579IBH- /home/drk/tillage/datasets/human/rna/encode/ENCSR033XWU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6374 RNA:CD4-positive, alpha-beta T cell male adult (20 years) +6376 ENCFF487XUM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR035SKV/summary/coverage+.w5 768 384 0.3 sum_sqrt 6377 RNA:gastroesophageal sphincter tissue female adult (51 years) +6377 ENCFF487XUM- /home/drk/tillage/datasets/human/rna/encode/ENCSR035SKV/summary/coverage-.w5 768 384 0.3 sum_sqrt 6376 RNA:gastroesophageal sphincter tissue female adult (51 years) +6378 ENCFF475JUK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR036SUN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6379 RNA:with mild cognitive impairment; middle frontal area 46 tissue female adult (90 or above years) +6379 ENCFF475JUK- /home/drk/tillage/datasets/human/rna/encode/ENCSR036SUN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6378 RNA:with mild cognitive impairment; middle frontal area 46 tissue female adult (90 or above years) +6380 ENCFF438BUG /home/drk/tillage/datasets/human/rna/encode/ENCSR038QZA/summary/coverage.w5 768 384 0.3 sum_sqrt 6380 RNA:with multiple sclerosis; naive thymus-derived CD4-positive, alpha-beta T cell +6381 ENCFF933QBC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR038WEK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6382 RNA:K562 membrane fraction +6382 ENCFF933QBC- /home/drk/tillage/datasets/human/rna/encode/ENCSR038WEK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6381 RNA:K562 membrane fraction +6383 ENCFF008CRB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR039ICU/summary/coverage+.w5 768 384 0.8734908657664815 sum_sqrt 6384 RNA:small intestine tissue female adult (30 years) +6384 ENCFF008CRB- /home/drk/tillage/datasets/human/rna/encode/ENCSR039ICU/summary/coverage-.w5 768 384 0.8734908657664815 sum_sqrt 6383 RNA:small intestine tissue female adult (30 years) +6385 ENCFF384MPW /home/drk/tillage/datasets/human/rna/encode/ENCSR039JPA/summary/coverage.w5 768 384 0.3 sum_sqrt 6385 RNA:with multiple sclerosis; immature natural killer cell +6386 ENCFF444LLL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR040YBR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6387 RNA:K562 nuclear fraction +6387 ENCFF444LLL- /home/drk/tillage/datasets/human/rna/encode/ENCSR040YBR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6386 RNA:K562 nuclear fraction +6388 ENCFF411VWO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR042GYH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6389 RNA:ovary tissue female adult (51 years) +6389 ENCFF411VWO- /home/drk/tillage/datasets/human/rna/encode/ENCSR042GYH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6388 RNA:ovary tissue female adult (51 years) +6390 ENCFF392VPC /home/drk/tillage/datasets/human/rna/encode/ENCSR042SVA/summary/coverage.w5 768 384 0.3 sum_sqrt 6390 RNA:with multiple sclerosis; naive thymus-derived CD4-positive, alpha-beta T cell +6391 ENCFF674RUW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR043KVA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6392 RNA:neurosphere embryo (15 weeks) originated from ganglionic eminence +6392 ENCFF674RUW- /home/drk/tillage/datasets/human/rna/encode/ENCSR043KVA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6391 RNA:neurosphere embryo (15 weeks) originated from ganglionic eminence +6393 ENCFF636VGI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR043RSE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6394 RNA:H1 +6394 ENCFF636VGI- /home/drk/tillage/datasets/human/rna/encode/ENCSR043RSE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6393 RNA:H1 +6395 ENCFF789CEJ /home/drk/tillage/datasets/human/rna/encode/ENCSR044JAQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6395 RNA:right lung tissue male embryo (105 days) +6396 ENCFF905NZB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR045GTF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6397 RNA:lung tissue female adult (47 years) +6397 ENCFF905NZB- /home/drk/tillage/datasets/human/rna/encode/ENCSR045GTF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6396 RNA:lung tissue female adult (47 years) +6398 ENCFF096UCI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR046XHI/summary/coverage+.w5 768 384 0.3 sum_sqrt 6399 RNA:ovary tissue female adult (47 years) +6399 ENCFF096UCI- /home/drk/tillage/datasets/human/rna/encode/ENCSR046XHI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6398 RNA:ovary tissue female adult (47 years) +6400 ENCFF639BWZ /home/drk/tillage/datasets/human/rna/encode/ENCSR047LLJ/summary/coverage.w5 768 384 0.3 sum_sqrt 6400 RNA:heart tissue male embryo (120 days) +6401 ENCFF638TAY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR051GPK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6402 RNA:neurosphere embryo (15 weeks) originated from ganglionic eminence +6402 ENCFF638TAY- /home/drk/tillage/datasets/human/rna/encode/ENCSR051GPK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6401 RNA:neurosphere embryo (15 weeks) originated from ganglionic eminence +6403 ENCFF804UGI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR051QXW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6404 RNA:chorionic villus tissue female embryo (40 weeks) +6404 ENCFF804UGI- /home/drk/tillage/datasets/human/rna/encode/ENCSR051QXW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6403 RNA:chorionic villus tissue female embryo (40 weeks) +6405 ENCFF652ISB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR052FJA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6406 RNA:smooth muscle cell originated from H9 +6406 ENCFF652ISB- /home/drk/tillage/datasets/human/rna/encode/ENCSR052FJA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6405 RNA:smooth muscle cell originated from H9 +6407 ENCFF196HWN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR052LON/summary/coverage+.w5 768 384 0.3 sum_sqrt 6408 RNA:middle frontal area 46 tissue male adult (71 years) +6408 ENCFF196HWN- /home/drk/tillage/datasets/human/rna/encode/ENCSR052LON/summary/coverage-.w5 768 384 0.3 sum_sqrt 6407 RNA:middle frontal area 46 tissue male adult (71 years) +6409 ENCFF205IED /home/drk/tillage/datasets/human/rna/encode/ENCSR056HPM/summary/coverage.w5 768 384 0.3 sum_sqrt 6409 RNA:K562 treated with 5 uM MB-3 for 12 hours +6410 ENCFF856SMT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR058OSL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6411 RNA:HepG2 nuclear fraction +6411 ENCFF856SMT- /home/drk/tillage/datasets/human/rna/encode/ENCSR058OSL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6410 RNA:HepG2 nuclear fraction +6412 ENCFF035GJD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR061HMO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6413 RNA:middle frontal area 46 tissue female adult (90 or above years) +6413 ENCFF035GJD- /home/drk/tillage/datasets/human/rna/encode/ENCSR061HMO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6412 RNA:middle frontal area 46 tissue female adult (90 or above years) +6414 ENCFF381TII+ /home/drk/tillage/datasets/human/rna/encode/ENCSR061RDC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6415 RNA:with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue female adult (87 years) +6415 ENCFF381TII- /home/drk/tillage/datasets/human/rna/encode/ENCSR061RDC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6414 RNA:with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue female adult (87 years) +6416 ENCFF994NAN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR061SFU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6417 RNA:HepG2 nuclear fraction +6417 ENCFF994NAN- /home/drk/tillage/datasets/human/rna/encode/ENCSR061SFU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6416 RNA:HepG2 nuclear fraction +6418 ENCFF127NDE /home/drk/tillage/datasets/human/rna/encode/ENCSR062FHL/summary/coverage.w5 768 384 0.3 sum_sqrt 6418 RNA:K562 treated with 1% DMSO for 4 hours +6419 ENCFF639UPM /home/drk/tillage/datasets/human/rna/encode/ENCSR066FZL/summary/coverage.w5 768 384 0.3 sum_sqrt 6419 RNA:large intestine tissue male embryo (108 days) +6420 ENCFF225USB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR067UNX/summary/coverage+.w5 768 384 0.3 sum_sqrt 6421 RNA:HT1080 nuclear fraction +6421 ENCFF225USB- /home/drk/tillage/datasets/human/rna/encode/ENCSR067UNX/summary/coverage-.w5 768 384 0.3 sum_sqrt 6420 RNA:HT1080 nuclear fraction +6422 ENCFF840VTO /home/drk/tillage/datasets/human/rna/encode/ENCSR069CMT/summary/coverage.w5 768 384 0.3 sum_sqrt 6422 RNA:thymus tissue male embryo (127 days) +6423 ENCFF656OUX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR071DYD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6424 RNA:pancreas tissue female child (16 years) +6424 ENCFF656OUX- /home/drk/tillage/datasets/human/rna/encode/ENCSR071DYD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6423 RNA:pancreas tissue female child (16 years) +6425 ENCFF432ENB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR071ZLM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6426 RNA:uterus tissue female adult (51 years) +6426 ENCFF432ENB- /home/drk/tillage/datasets/human/rna/encode/ENCSR071ZLM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6425 RNA:uterus tissue female adult (51 years) +6427 ENCFF906FBF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR071ZMO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6428 RNA:kidney tissue male adult (41 years) +6428 ENCFF906FBF- /home/drk/tillage/datasets/human/rna/encode/ENCSR071ZMO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6427 RNA:kidney tissue male adult (41 years) +6429 ENCFF480GYV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR073XFZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6430 RNA:OCI-LY7 +6430 ENCFF480GYV- /home/drk/tillage/datasets/human/rna/encode/ENCSR073XFZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6429 RNA:OCI-LY7 +6431 ENCFF432CYV /home/drk/tillage/datasets/human/rna/encode/ENCSR074APH/summary/coverage.w5 768 384 0.3 sum_sqrt 6431 RNA:right lung tissue female embryo (98 days) +6432 ENCFF434LID+ /home/drk/tillage/datasets/human/rna/encode/ENCSR074FTH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6433 RNA:spleen tissue male adult (26 years) +6433 ENCFF434LID- /home/drk/tillage/datasets/human/rna/encode/ENCSR074FTH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6432 RNA:spleen tissue male adult (26 years) +6434 ENCFF073NKN /home/drk/tillage/datasets/human/rna/encode/ENCSR077AZT/summary/coverage.w5 768 384 0.3 sum_sqrt 6434 RNA:GM12878 +6435 ENCFF847OUD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR080HPT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6436 RNA:omental fat pad tissue male adult (54 years) +6436 ENCFF847OUD- /home/drk/tillage/datasets/human/rna/encode/ENCSR080HPT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6435 RNA:omental fat pad tissue male adult (54 years) +6437 ENCFF521SQI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR085HNI/summary/coverage+.w5 768 384 0.3 sum_sqrt 6438 RNA:liver tissue male adult (18 years) +6438 ENCFF521SQI- /home/drk/tillage/datasets/human/rna/encode/ENCSR085HNI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6437 RNA:liver tissue male adult (18 years) +6439 ENCFF884CFC /home/drk/tillage/datasets/human/rna/encode/ENCSR086DZF/summary/coverage.w5 768 384 0.3 sum_sqrt 6439 RNA:muscle of leg tissue male embryo (96 days) +6440 ENCFF894JRG /home/drk/tillage/datasets/human/rna/encode/ENCSR092CNB/summary/coverage.w5 768 384 0.3 sum_sqrt 6440 RNA:IgD-negative memory B cell +6441 ENCFF865FLR /home/drk/tillage/datasets/human/rna/encode/ENCSR092KKW/summary/coverage.w5 768 384 0.3 sum_sqrt 6441 RNA:with multiple sclerosis; naive thymus-derived CD4-positive, alpha-beta T cell +6442 ENCFF387UUZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR094GVZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6443 RNA:sigmoid colon tissue female adult (53 years) +6443 ENCFF387UUZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR094GVZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6442 RNA:sigmoid colon tissue female adult (53 years) +6444 ENCFF430LQC /home/drk/tillage/datasets/human/rna/encode/ENCSR094RGI/summary/coverage.w5 768 384 0.3 sum_sqrt 6444 RNA:muscle of back tissue male embryo (96 days) +6445 ENCFF863UAA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR094VRQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6446 RNA:breast epithelium tissue male adult (37 years) +6446 ENCFF863UAA- /home/drk/tillage/datasets/human/rna/encode/ENCSR094VRQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6445 RNA:breast epithelium tissue male adult (37 years) +6447 ENCFF942QIE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR096LTX/summary/coverage+.w5 768 384 0.3 sum_sqrt 6448 RNA:spleen tissue female adult (61 years) +6448 ENCFF942QIE- /home/drk/tillage/datasets/human/rna/encode/ENCSR096LTX/summary/coverage-.w5 768 384 0.3 sum_sqrt 6447 RNA:spleen tissue female adult (61 years) +6449 ENCFF656PZD /home/drk/tillage/datasets/human/rna/encode/ENCSR096USV/summary/coverage.w5 768 384 0.3 sum_sqrt 6449 RNA:muscle of leg tissue male embryo (127 days) +6450 ENCFF071TXL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR098BUF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6451 RNA:esophagus muscularis mucosa tissue female adult (53 years) +6451 ENCFF071TXL- /home/drk/tillage/datasets/human/rna/encode/ENCSR098BUF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6450 RNA:esophagus muscularis mucosa tissue female adult (53 years) +6452 ENCFF710BHJ /home/drk/tillage/datasets/human/rna/encode/ENCSR100JNS/summary/coverage.w5 768 384 0.3 sum_sqrt 6452 RNA:K562 treated with 1% DMSO for 24 hours +6453 ENCFF689GBG /home/drk/tillage/datasets/human/rna/encode/ENCSR100VUY/summary/coverage.w5 768 384 0.3 sum_sqrt 6453 RNA:K562 treated with 10 nM Chaetocin for 24 hours +6454 ENCFF988EBT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR102TQN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6455 RNA:esophagus tissue male adult (34 years) +6455 ENCFF988EBT- /home/drk/tillage/datasets/human/rna/encode/ENCSR102TQN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6454 RNA:esophagus tissue male adult (34 years) +6456 ENCFF056NWD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR104ZDH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6457 RNA:placental basal plate tissue embryo (16 weeks) +6457 ENCFF056NWD- /home/drk/tillage/datasets/human/rna/encode/ENCSR104ZDH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6456 RNA:placental basal plate tissue embryo (16 weeks) +6458 ENCFF876APW /home/drk/tillage/datasets/human/rna/encode/ENCSR105NQB/summary/coverage.w5 768 384 0.3 sum_sqrt 6458 RNA:K562 treated with 7.5 nM Vorinostat for 12 hours +6459 ENCFF507FAA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR106SZN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6460 RNA:spleen tissue male adult (54 years) +6460 ENCFF507FAA- /home/drk/tillage/datasets/human/rna/encode/ENCSR106SZN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6459 RNA:spleen tissue male adult (54 years) +6461 ENCFF136YVC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR108MAU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6462 RNA:suprapubic skin tissue male adult (54 years) +6462 ENCFF136YVC- /home/drk/tillage/datasets/human/rna/encode/ENCSR108MAU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6461 RNA:suprapubic skin tissue male adult (54 years) +6463 ENCFF478XYM /home/drk/tillage/datasets/human/rna/encode/ENCSR108XUM/summary/coverage.w5 768 384 0.3 sum_sqrt 6463 RNA:naive thymus-derived CD4-positive, alpha-beta T cell +6464 ENCFF944XYT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR109IQO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6465 RNA:K562 +6465 ENCFF944XYT- /home/drk/tillage/datasets/human/rna/encode/ENCSR109IQO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6464 RNA:K562 +6466 ENCFF417PPZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR110BDY/summary/coverage+.w5 768 384 0.3 sum_sqrt 6467 RNA:cardiac atrium fibroblast male child (2 years) +6467 ENCFF417PPZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR110BDY/summary/coverage-.w5 768 384 0.3 sum_sqrt 6466 RNA:cardiac atrium fibroblast male child (2 years) +6468 ENCFF122XJD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR111PSY/summary/coverage+.w5 768 384 0.3 sum_sqrt 6469 RNA:activated T-cell male adult (42 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours +6469 ENCFF122XJD- /home/drk/tillage/datasets/human/rna/encode/ENCSR111PSY/summary/coverage-.w5 768 384 0.3 sum_sqrt 6468 RNA:activated T-cell male adult (42 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours +6470 ENCFF823LKJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR113HQM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6471 RNA:uterus tissue female adult (53 years) +6471 ENCFF823LKJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR113HQM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6470 RNA:uterus tissue female adult (53 years) +6472 ENCFF385SAC /home/drk/tillage/datasets/human/rna/encode/ENCSR114LNC/summary/coverage.w5 768 384 0.3 sum_sqrt 6472 RNA:K562 treated with 7.5 nM Vorinostat for 4 hours +6473 ENCFF132EEP /home/drk/tillage/datasets/human/rna/encode/ENCSR115PIZ/summary/coverage.w5 768 384 0.3 sum_sqrt 6473 RNA:K562 treated with 10 nM Chaetocin for 48 hours +6474 ENCFF767MLU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR118TVR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6475 RNA:epithelial cell of proximal tubule +6475 ENCFF767MLU- /home/drk/tillage/datasets/human/rna/encode/ENCSR118TVR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6474 RNA:epithelial cell of proximal tubule +6476 ENCFF195SMK /home/drk/tillage/datasets/human/rna/encode/ENCSR120NEA/summary/coverage.w5 768 384 0.3 sum_sqrt 6476 RNA:adrenal gland tissue female embryo (85 days) +6477 ENCFF996KKA /home/drk/tillage/datasets/human/rna/encode/ENCSR123ZCX/summary/coverage.w5 768 384 0.3 sum_sqrt 6477 RNA:stomach tissue male embryo (127 days) +6478 ENCFF642WCG /home/drk/tillage/datasets/human/rna/encode/ENCSR124KOZ/summary/coverage.w5 768 384 0.3 sum_sqrt 6478 RNA:K562 treated with 25 uM Galeterone for 24 hours +6479 ENCFF669XAP /home/drk/tillage/datasets/human/rna/encode/ENCSR125NGM/summary/coverage.w5 768 384 0.3 sum_sqrt 6479 RNA:left renal cortex interstitium tissue male embryo (105 days) +6480 ENCFF962EZE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR128CYL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6481 RNA:Panc1 +6481 ENCFF962EZE- /home/drk/tillage/datasets/human/rna/encode/ENCSR128CYL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6480 RNA:Panc1 +6482 ENCFF310GNU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR129KCJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6483 RNA:lung tissue female adult (30 years) +6483 ENCFF310GNU- /home/drk/tillage/datasets/human/rna/encode/ENCSR129KCJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6482 RNA:lung tissue female adult (30 years) +6484 ENCFF849ELK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR129VBC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6485 RNA:astrocyte +6485 ENCFF849ELK- /home/drk/tillage/datasets/human/rna/encode/ENCSR129VBC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6484 RNA:astrocyte +6486 ENCFF568EVH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR130TZW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6487 RNA:posterior vena cava tissue female adult (47 years) +6487 ENCFF568EVH- /home/drk/tillage/datasets/human/rna/encode/ENCSR130TZW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6486 RNA:posterior vena cava tissue female adult (47 years) +6488 ENCFF198IBF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR132VGJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6489 RNA:Right ventricle myocardium superior tissue male adult (60 years) +6489 ENCFF198IBF- /home/drk/tillage/datasets/human/rna/encode/ENCSR132VGJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6488 RNA:Right ventricle myocardium superior tissue male adult (60 years) +6490 ENCFF565QRM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR135IAL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6491 RNA:right lobe of liver tissue female adult (41 years) +6491 ENCFF565QRM- /home/drk/tillage/datasets/human/rna/encode/ENCSR135IAL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6490 RNA:right lobe of liver tissue female adult (41 years) +6492 ENCFF117HUT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR136WGP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6493 RNA:SK-N-DZ treated with dimethyl sulfoxide for 72 hours +6493 ENCFF117HUT- /home/drk/tillage/datasets/human/rna/encode/ENCSR136WGP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6492 RNA:SK-N-DZ treated with dimethyl sulfoxide for 72 hours +6494 ENCFF105TXB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR140DCD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6495 RNA:ovary tissue female adult (46 years) +6495 ENCFF105TXB- /home/drk/tillage/datasets/human/rna/encode/ENCSR140DCD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6494 RNA:ovary tissue female adult (46 years) +6496 ENCFF688KBA /home/drk/tillage/datasets/human/rna/encode/ENCSR144UVO/summary/coverage.w5 768 384 0.3 sum_sqrt 6496 RNA:muscle of leg tissue male embryo (105 days) +6497 ENCFF477AQU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR146LBD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6498 RNA:vagina tissue female adult (53 years) +6498 ENCFF477AQU- /home/drk/tillage/datasets/human/rna/encode/ENCSR146LBD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6497 RNA:vagina tissue female adult (53 years) +6499 ENCFF561SVV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR146ZKR/summary/coverage+.w5 768 384 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/home/drk/tillage/datasets/human/rna/encode/ENCSR150QJY/summary/coverage-.w5 768 384 0.3 sum_sqrt 6510 RNA:subcutaneous adipose tissue tissue female adult (51 years) +6512 ENCFF535NFF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR151FXS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6513 RNA:CD8-positive, alpha-beta T cell male adult (21 years) +6513 ENCFF535NFF- /home/drk/tillage/datasets/human/rna/encode/ENCSR151FXS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6512 RNA:CD8-positive, alpha-beta T cell male adult (21 years) +6514 ENCFF782HFV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR151NGC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6515 RNA:GM12878 +6515 ENCFF782HFV- /home/drk/tillage/datasets/human/rna/encode/ENCSR151NGC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6514 RNA:GM12878 +6516 ENCFF259EXX /home/drk/tillage/datasets/human/rna/encode/ENCSR152BBF/summary/coverage.w5 768 384 0.3 sum_sqrt 6516 RNA:naive thymus-derived CD8-positive, alpha-beta T cell +6517 ENCFF969VXC+ 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adult (51 years) +6523 ENCFF900MLZ /home/drk/tillage/datasets/human/rna/encode/ENCSR158XIJ/summary/coverage.w5 768 384 0.3 sum_sqrt 6523 RNA:thymus tissue female embryo (98 days) +6524 ENCFF664RDQ /home/drk/tillage/datasets/human/rna/encode/ENCSR159UIB/summary/coverage.w5 768 384 0.3 sum_sqrt 6524 RNA:with multiple sclerosis; naive thymus-derived CD8-positive, alpha-beta T cell +6525 ENCFF881ITI /home/drk/tillage/datasets/human/rna/encode/ENCSR160UAZ/summary/coverage.w5 768 384 0.3 sum_sqrt 6525 RNA:left renal pelvis tissue male embryo (105 days) +6526 ENCFF219KLR /home/drk/tillage/datasets/human/rna/encode/ENCSR161RSX/summary/coverage.w5 768 384 0.3 sum_sqrt 6526 RNA:K562 treated with 5 uM MB-3 for 24 hours +6527 ENCFF695GPR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR164OCT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6528 RNA:NCI-H460 +6528 ENCFF695GPR- /home/drk/tillage/datasets/human/rna/encode/ENCSR164OCT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6527 RNA:NCI-H460 +6529 ENCFF179DDD /home/drk/tillage/datasets/human/rna/encode/ENCSR165EQJ/summary/coverage.w5 768 384 0.3 sum_sqrt 6529 RNA:K562 treated with 5 uM MB-3 for 4 hours +6530 ENCFF013IKJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR165QTZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6531 RNA:pancreas tissue female adult (61 years) +6531 ENCFF013IKJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR165QTZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6530 RNA:pancreas tissue female adult (61 years) +6532 ENCFF681MQA /home/drk/tillage/datasets/human/rna/encode/ENCSR166IFS/summary/coverage.w5 768 384 0.3 sum_sqrt 6532 RNA:WTC11 genetically modified (insertion) using TALEN inserting M. musculus Neurog2 +6533 ENCFF686YTX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR166QLP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6534 RNA:HT1080 cytosolic fraction +6534 ENCFF686YTX- /home/drk/tillage/datasets/human/rna/encode/ENCSR166QLP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6533 RNA:HT1080 cytosolic fraction 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ENCFF060EGL- /home/drk/tillage/datasets/human/rna/encode/ENCSR176FKY/summary/coverage-.w5 768 384 0.3 sum_sqrt 6540 RNA:trophoblast tissue male embryo (38 weeks) +6542 ENCFF817FWU /home/drk/tillage/datasets/human/rna/encode/ENCSR176WMG/summary/coverage.w5 768 384 0.3 sum_sqrt 6542 RNA:right lung tissue male embryo (96 days) +6543 ENCFF014YFU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR177XCG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6544 RNA:CD4-positive, alpha-beta memory T cell male adult (43 years) +6544 ENCFF014YFU- /home/drk/tillage/datasets/human/rna/encode/ENCSR177XCG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6543 RNA:CD4-positive, alpha-beta memory T cell male adult (43 years) +6545 ENCFF581ZGH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR181ZGR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6546 RNA:HepG2 +6546 ENCFF581ZGH- /home/drk/tillage/datasets/human/rna/encode/ENCSR181ZGR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6545 RNA:HepG2 +6547 ENCFF741HPN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR182CBU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6548 RNA:esophagus muscularis mucosa tissue male adult (37 years) +6548 ENCFF741HPN- /home/drk/tillage/datasets/human/rna/encode/ENCSR182CBU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6547 RNA:esophagus muscularis mucosa tissue male adult (37 years) +6549 ENCFF837ZJA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR184LTL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6550 RNA:mucosa of descending colon tissue female adult (61 years) +6550 ENCFF837ZJA- /home/drk/tillage/datasets/human/rna/encode/ENCSR184LTL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6549 RNA:mucosa of descending colon tissue female adult (61 years) +6551 ENCFF542TGZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR185TQB/summary/coverage+.w5 768 384 0.3 sum_sqrt 6552 RNA:aorta tissue female adult (41 years) +6552 ENCFF542TGZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR185TQB/summary/coverage-.w5 768 384 0.3 sum_sqrt 6551 RNA:aorta tissue female adult (41 years) +6553 ENCFF046XIT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR192NBO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6554 RNA:fibroblast of breast female adult (17 years) +6554 ENCFF046XIT- /home/drk/tillage/datasets/human/rna/encode/ENCSR192NBO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6553 RNA:fibroblast of breast female adult (17 years) +6555 ENCFF371QSS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR194HVU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6556 RNA:spleen tissue female adult (51 years) +6556 ENCFF371QSS- /home/drk/tillage/datasets/human/rna/encode/ENCSR194HVU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6555 RNA:spleen tissue female adult (51 years) +6557 ENCFF574YPE /home/drk/tillage/datasets/human/rna/encode/ENCSR195JRH/summary/coverage.w5 768 384 0.3 sum_sqrt 6557 RNA:K562 treated with 5 uM JQ1 for 12 hours +6558 ENCFF826YBE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR196ARY/summary/coverage+.w5 768 384 0.3 sum_sqrt 6559 RNA:fibroblast of breast female adult (26 years) +6559 ENCFF826YBE- /home/drk/tillage/datasets/human/rna/encode/ENCSR196ARY/summary/coverage-.w5 768 384 0.3 sum_sqrt 6558 RNA:fibroblast of breast female adult (26 years) +6560 ENCFF424DIT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR198QAJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6561 RNA:middle frontal area 46 tissue female adult (90 or above years) +6561 ENCFF424DIT- /home/drk/tillage/datasets/human/rna/encode/ENCSR198QAJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6560 RNA:middle frontal area 46 tissue female adult (90 or above years) +6562 ENCFF346QDJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR198TKA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6563 RNA:mesangial cell NONE and female embryo (21 weeks) +6563 ENCFF346QDJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR198TKA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6562 RNA:mesangial cell NONE and female embryo (21 weeks) +6564 ENCFF117JSP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR201WVA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6565 RNA:SK-MEL-5 nuclear fraction +6565 ENCFF117JSP- /home/drk/tillage/datasets/human/rna/encode/ENCSR201WVA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6564 RNA:SK-MEL-5 nuclear fraction +6566 ENCFF290PRJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR201XOZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6567 RNA:adrenal gland tissue female child (16 years) +6567 ENCFF290PRJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR201XOZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6566 RNA:adrenal gland tissue female child (16 years) +6568 ENCFF767NPP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR202OWR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6569 RNA:colonic mucosa tissue female adult (41 years) +6569 ENCFF767NPP- /home/drk/tillage/datasets/human/rna/encode/ENCSR202OWR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6568 RNA:colonic mucosa tissue female adult (41 years) +6570 ENCFF693TJD /home/drk/tillage/datasets/human/rna/encode/ENCSR204XBB/summary/coverage.w5 768 384 0.3 sum_sqrt 6570 RNA:renal pelvis tissue female embryo (105 days) +6571 ENCFF117CTU /home/drk/tillage/datasets/human/rna/encode/ENCSR206KFV/summary/coverage.w5 768 384 0.3 sum_sqrt 6571 RNA:K562 treated with 25 uM Galeterone for 4 hours +6572 ENCFF259TIE /home/drk/tillage/datasets/human/rna/encode/ENCSR211CKX/summary/coverage.w5 768 384 0.3 sum_sqrt 6572 RNA:with multiple sclerosis; naive thymus-derived CD8-positive, alpha-beta T cell +6573 ENCFF064TTU /home/drk/tillage/datasets/human/rna/encode/ENCSR212AMA/summary/coverage.w5 768 384 0.3 sum_sqrt 6573 RNA:kidney tissue female embryo (105 days) +6574 ENCFF772RIQ /home/drk/tillage/datasets/human/rna/encode/ENCSR214NBT/summary/coverage.w5 768 384 0.3 sum_sqrt 6574 RNA:CD4-positive, CD25-positive, alpha-beta regulatory T cell +6575 ENCFF648RBX /home/drk/tillage/datasets/human/rna/encode/ENCSR222IGR/summary/coverage.w5 768 384 0.3 sum_sqrt 6575 RNA:left lung tissue male embryo (96 days) +6576 ENCFF057IIF /home/drk/tillage/datasets/human/rna/encode/ENCSR223DWL/summary/coverage.w5 768 384 0.3 sum_sqrt 6576 RNA:K562 treated with 10 nM Bortezomib for 48 hours +6577 ENCFF470OCI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR224HFZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6578 RNA:myoepithelial cell of mammary gland female adult (22 years) +6578 ENCFF470OCI- /home/drk/tillage/datasets/human/rna/encode/ENCSR224HFZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6577 RNA:myoepithelial cell of mammary gland female adult (22 years) +6579 ENCFF103EZF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR226KML/summary/coverage+.w5 768 384 0.3 sum_sqrt 6580 RNA:right lobe of liver tissue female adult (53 years) +6580 ENCFF103EZF- /home/drk/tillage/datasets/human/rna/encode/ENCSR226KML/summary/coverage-.w5 768 384 0.3 sum_sqrt 6579 RNA:right lobe of liver tissue female adult (53 years) +6581 ENCFF367DUO /home/drk/tillage/datasets/human/rna/encode/ENCSR229JRA/summary/coverage.w5 768 384 0.3 sum_sqrt 6581 RNA:thymus tissue female embryo (113 days) +6582 ENCFF128YXB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR229LFK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6583 RNA:right lobe of liver tissue female child (16 years) +6583 ENCFF128YXB- /home/drk/tillage/datasets/human/rna/encode/ENCSR229LFK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6582 RNA:right lobe of liver tissue female child (16 years) +6584 ENCFF401TVK /home/drk/tillage/datasets/human/rna/encode/ENCSR230KVL/summary/coverage.w5 768 384 0.3 sum_sqrt 6584 RNA:naive thymus-derived CD8-positive, alpha-beta T cell +6585 ENCFF155PJH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR233IJT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6586 RNA:astrocyte +6586 ENCFF155PJH- /home/drk/tillage/datasets/human/rna/encode/ENCSR233IJT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6585 RNA:astrocyte +6587 ENCFF625DRX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR236OON/summary/coverage+.w5 768 384 0.3 sum_sqrt 6588 RNA:adipose tissue tissue female adult (63 years) +6588 ENCFF625DRX- /home/drk/tillage/datasets/human/rna/encode/ENCSR236OON/summary/coverage-.w5 768 384 0.3 sum_sqrt 6587 RNA:adipose tissue tissue female adult (63 years) +6589 ENCFF312VKB /home/drk/tillage/datasets/human/rna/encode/ENCSR236URT/summary/coverage.w5 768 384 0.3 sum_sqrt 6589 RNA:smooth muscle cell originated from H9 +6590 ENCFF837FLM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR238ZZD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6591 RNA:thyroid gland tissue female adult (53 years) +6591 ENCFF837FLM- /home/drk/tillage/datasets/human/rna/encode/ENCSR238ZZD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6590 RNA:thyroid gland tissue female adult (53 years) +6592 ENCFF641YCY /home/drk/tillage/datasets/human/rna/encode/ENCSR239BBI/summary/coverage.w5 768 384 0.3 sum_sqrt 6592 RNA:muscle of back tissue female embryo (85 days) 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RNA:neural progenitor cell originated from H9 +6599 ENCFF908VIH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR245ATJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6600 RNA:HepG2 +6600 ENCFF908VIH- /home/drk/tillage/datasets/human/rna/encode/ENCSR245ATJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6599 RNA:HepG2 +6601 ENCFF381OQK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR249CKG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6602 RNA:chorion tissue embryo (16 weeks) +6602 ENCFF381OQK- /home/drk/tillage/datasets/human/rna/encode/ENCSR249CKG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6601 RNA:chorion tissue embryo (16 weeks) +6603 ENCFF645AYP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR252UHW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6604 RNA:heart right ventricle tissue female adult (46 years) +6604 ENCFF645AYP- /home/drk/tillage/datasets/human/rna/encode/ENCSR252UHW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6603 RNA:heart right ventricle tissue female adult (46 years) +6605 ENCFF196LHX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR254JJM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6606 RNA:Daoy +6606 ENCFF196LHX- /home/drk/tillage/datasets/human/rna/encode/ENCSR254JJM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6605 RNA:Daoy +6607 ENCFF770TOE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR255NYQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6608 RNA:SK-N-DZ nuclear fraction +6608 ENCFF770TOE- /home/drk/tillage/datasets/human/rna/encode/ENCSR255NYQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6607 RNA:SK-N-DZ nuclear fraction +6609 ENCFF615IJV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR256YHI/summary/coverage+.w5 768 384 0.3 sum_sqrt 6610 RNA:neurosphere embryo (15 weeks) originated from cortex +6610 ENCFF615IJV- /home/drk/tillage/datasets/human/rna/encode/ENCSR256YHI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6609 RNA:neurosphere embryo (15 weeks) originated from cortex +6611 ENCFF666KUJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR257NIR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6612 RNA:Peyer's patch tissue male adult (54 years) +6612 ENCFF666KUJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR257NIR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6611 RNA:Peyer's patch tissue male adult (54 years) +6613 ENCFF239BUM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR258ELN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6614 RNA:spleen tissue female adult (59 years) +6614 ENCFF239BUM- /home/drk/tillage/datasets/human/rna/encode/ENCSR258ELN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6613 RNA:spleen tissue female adult (59 years) +6615 ENCFF744TRY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR261ISO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6616 RNA:foreskin fibroblast male newborn +6616 ENCFF744TRY- /home/drk/tillage/datasets/human/rna/encode/ENCSR261ISO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6615 RNA:foreskin fibroblast male newborn +6617 ENCFF583FIC /home/drk/tillage/datasets/human/rna/encode/ENCSR264IXQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6617 RNA:K562 treated with 10 uM AR-42 for 4 hours +6618 ENCFF946ZPT /home/drk/tillage/datasets/human/rna/encode/ENCSR264LON/summary/coverage.w5 768 384 0.3 sum_sqrt 6618 RNA:with multiple sclerosis; CD14-positive monocyte +6619 ENCFF393ZMQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR264VJN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6620 RNA:activated CD8-positive, alpha-beta T cell male adult (21 years) treated with anti-CD3 and anti-CD28 coated beads +6620 ENCFF393ZMQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR264VJN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6619 RNA:activated CD8-positive, alpha-beta T cell male adult (21 years) treated with anti-CD3 and anti-CD28 coated beads +6621 ENCFF315BLU /home/drk/tillage/datasets/human/rna/encode/ENCSR265NZF/summary/coverage.w5 768 384 0.3 sum_sqrt 6621 RNA:spleen tissue embryo (112 days) +6622 ENCFF313KNT /home/drk/tillage/datasets/human/rna/encode/ENCSR266LHQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6622 RNA:CD4-positive, alpha-beta memory T cell +6623 ENCFF474WFJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR266PVZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6624 RNA:right cardiac atrium tissue female adult (46 years) +6624 ENCFF474WFJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR266PVZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6623 RNA:right cardiac atrium tissue female adult (46 years) +6625 ENCFF670MHR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR266XAJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6626 RNA:endodermal cell +6626 ENCFF670MHR- /home/drk/tillage/datasets/human/rna/encode/ENCSR266XAJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6625 RNA:endodermal cell +6627 ENCFF864IDH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR270OKS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6628 RNA:sigmoid colon tissue male adult (21 years) +6628 ENCFF864IDH- /home/drk/tillage/datasets/human/rna/encode/ENCSR270OKS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6627 RNA:sigmoid colon tissue male adult (21 years) +6629 ENCFF506SFB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR270XRV/summary/coverage+.w5 768 384 0.3 sum_sqrt 6630 RNA:keratinocyte female +6630 ENCFF506SFB- /home/drk/tillage/datasets/human/rna/encode/ENCSR270XRV/summary/coverage-.w5 768 384 0.3 sum_sqrt 6629 RNA:keratinocyte female +6631 ENCFF533JTF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR271DJJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6632 RNA:endocrine pancreas tissue adult (59 years) +6632 ENCFF533JTF- /home/drk/tillage/datasets/human/rna/encode/ENCSR271DJJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6631 RNA:endocrine pancreas tissue adult (59 years) +6633 ENCFF281UGH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR272UNO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6634 RNA:tibial nerve tissue female adult (51 years) +6634 ENCFF281UGH- /home/drk/tillage/datasets/human/rna/encode/ENCSR272UNO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6633 RNA:tibial nerve tissue female adult (51 years) +6635 ENCFF637ZBG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR274JRR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6636 RNA:brain tissue female adult (66 years) +6636 ENCFF637ZBG- /home/drk/tillage/datasets/human/rna/encode/ENCSR274JRR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6635 RNA:brain tissue female adult (66 years) +6637 ENCFF587USA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR275JSL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6638 RNA:with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue male adult (73 years) +6638 ENCFF587USA- /home/drk/tillage/datasets/human/rna/encode/ENCSR275JSL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6637 RNA:with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue male adult (73 years) +6639 ENCFF392DAR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR275ZLF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6640 RNA:mesenchymal stem cell originated from H1 +6640 ENCFF392DAR- /home/drk/tillage/datasets/human/rna/encode/ENCSR275ZLF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6639 RNA:mesenchymal stem cell originated from H1 +6641 ENCFF037OMX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR276MMH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6642 RNA:adrenal gland tissue male adult (37 years) +6642 ENCFF037OMX- /home/drk/tillage/datasets/human/rna/encode/ENCSR276MMH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6641 RNA:adrenal gland tissue male adult (37 years) +6643 ENCFF565FPI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR278UYN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6644 RNA:lung tissue male child (3 years) +6644 ENCFF565FPI- /home/drk/tillage/datasets/human/rna/encode/ENCSR278UYN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6643 RNA:lung tissue male child (3 years) +6645 ENCFF496QEP /home/drk/tillage/datasets/human/rna/encode/ENCSR279VNR/summary/coverage.w5 768 384 0.3 sum_sqrt 6645 RNA:CD8-positive, alpha-beta memory T cell +6646 ENCFF547YEW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR282GZU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6647 RNA:stimulated activated CD8-positive, alpha-beta T cell male adult (21 years) treated with 10 ng/mL Interleukin-2, anti-CD3 and anti-CD28 coated beads +6647 ENCFF547YEW- /home/drk/tillage/datasets/human/rna/encode/ENCSR282GZU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6646 RNA:stimulated activated CD8-positive, alpha-beta T cell male adult (21 years) treated with 10 ng/mL Interleukin-2, anti-CD3 and anti-CD28 coated beads +6648 ENCFF295JCA /home/drk/tillage/datasets/human/rna/encode/ENCSR286KWP/summary/coverage.w5 768 384 0.3 sum_sqrt 6648 RNA:large intestine tissue male embryo (115 days) +6649 ENCFF719RAL /home/drk/tillage/datasets/human/rna/encode/ENCSR287DHQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6649 RNA:K562 treated with 10 nM Bortezomib for 12 hours +6650 ENCFF189MNY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR288RRZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6651 RNA:placenta tissue male embryo +6651 ENCFF189MNY- /home/drk/tillage/datasets/human/rna/encode/ENCSR288RRZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6650 RNA:placenta tissue male embryo +6652 ENCFF634JRF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR290IHM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6653 RNA:middle frontal area 46 tissue female adult (79 years) +6653 ENCFF634JRF- /home/drk/tillage/datasets/human/rna/encode/ENCSR290IHM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6652 RNA:middle frontal area 46 tissue female adult (79 years) +6654 ENCFF960QLH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR291DJH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6655 RNA:SK-MEL-5 cytosolic fraction +6655 ENCFF960QLH- /home/drk/tillage/datasets/human/rna/encode/ENCSR291DJH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6654 RNA:SK-MEL-5 cytosolic fraction +6656 ENCFF185NBE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR291TRJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6657 RNA:endodermal cell +6657 ENCFF185NBE- /home/drk/tillage/datasets/human/rna/encode/ENCSR291TRJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6656 RNA:endodermal cell +6658 ENCFF986WTF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR292TAP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6659 RNA:neural cell originated from H1 +6659 ENCFF986WTF- /home/drk/tillage/datasets/human/rna/encode/ENCSR292TAP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6658 RNA:neural cell originated from H1 +6660 ENCFF030JXK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR292TYT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6661 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (90 or above years) +6661 ENCFF030JXK- /home/drk/tillage/datasets/human/rna/encode/ENCSR292TYT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6660 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (90 or above years) +6662 ENCFF713REM /home/drk/tillage/datasets/human/rna/encode/ENCSR294NDO/summary/coverage.w5 768 384 0.3 sum_sqrt 6662 RNA:cardiac muscle cell originated from RUES2 +6663 ENCFF151AEP /home/drk/tillage/datasets/human/rna/encode/ENCSR296LJV/summary/coverage.w5 768 384 0.3 sum_sqrt 6663 RNA:CD4-positive, alpha-beta memory T cell +6664 ENCFF145OAS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR296PMS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6665 RNA:stomach tissue male adult (54 years) +6665 ENCFF145OAS- /home/drk/tillage/datasets/human/rna/encode/ENCSR296PMS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6664 RNA:stomach tissue male adult (54 years) +6666 ENCFF430DVF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR297AZN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6667 RNA:CD4-positive, alpha-beta memory T cell male adult (43 years) +6667 ENCFF430DVF- /home/drk/tillage/datasets/human/rna/encode/ENCSR297AZN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6666 RNA:CD4-positive, alpha-beta memory T cell male adult (43 years) +6668 ENCFF047KOP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR297UBP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6669 RNA:GM12878 +6669 ENCFF047KOP- /home/drk/tillage/datasets/human/rna/encode/ENCSR297UBP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6668 RNA:GM12878 +6670 ENCFF557CLI /home/drk/tillage/datasets/human/rna/encode/ENCSR303IRE/summary/coverage.w5 768 384 0.3 sum_sqrt 6670 RNA:K562 treated with 7.5 nM Panobinostat for 48 hours +6671 ENCFF119XJG /home/drk/tillage/datasets/human/rna/encode/ENCSR305NXN/summary/coverage.w5 768 384 0.3 sum_sqrt 6671 RNA:muscle of arm tissue male embryo (127 days) +6672 ENCFF624DSV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR306IAW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6673 RNA:T-cell male adult (42 years) +6673 ENCFF624DSV- /home/drk/tillage/datasets/human/rna/encode/ENCSR306IAW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6672 RNA:T-cell male adult (42 years) +6674 ENCFF560YUT /home/drk/tillage/datasets/human/rna/encode/ENCSR307FAG/summary/coverage.w5 768 384 0.3 sum_sqrt 6674 RNA:naive B cell +6675 ENCFF597XJZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR308XAR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6676 RNA:placenta tissue male embryo +6676 ENCFF597XJZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR308XAR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6675 RNA:placenta tissue male embryo +6677 ENCFF138GLV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR313COD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6678 RNA:upper lobe of left lung tissue male adult (37 years) +6678 ENCFF138GLV- /home/drk/tillage/datasets/human/rna/encode/ENCSR313COD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6677 RNA:upper lobe of left lung tissue male adult (37 years) +6679 ENCFF816BKU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR313TJR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6680 RNA:peripheral blood mononuclear cell female adult (28 years) +6680 ENCFF816BKU- /home/drk/tillage/datasets/human/rna/encode/ENCSR313TJR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6679 RNA:peripheral blood mononuclear cell female adult (28 years) +6681 ENCFF505JCK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR314LXG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6682 RNA:Karpas-422 +6682 ENCFF505JCK- /home/drk/tillage/datasets/human/rna/encode/ENCSR314LXG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6681 RNA:Karpas-422 +6683 ENCFF359ITR /home/drk/tillage/datasets/human/rna/encode/ENCSR317LMH/summary/coverage.w5 768 384 0.3 sum_sqrt 6683 RNA:muscle of arm tissue female embryo (98 days) +6684 ENCFF629XGV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR320BRR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6685 RNA:RPMI7951 +6685 ENCFF629XGV- /home/drk/tillage/datasets/human/rna/encode/ENCSR320BRR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6684 RNA:RPMI7951 +6686 ENCFF649MKX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR320OTJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6687 RNA:ovary tissue female adult (41 years) +6687 ENCFF649MKX- /home/drk/tillage/datasets/human/rna/encode/ENCSR320OTJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6686 RNA:ovary tissue female adult (41 years) +6688 ENCFF596HNR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR321PGV/summary/coverage+.w5 768 384 0.3 sum_sqrt 6689 RNA:lower leg skin tissue male adult (37 years) +6689 ENCFF596HNR- /home/drk/tillage/datasets/human/rna/encode/ENCSR321PGV/summary/coverage-.w5 768 384 0.3 sum_sqrt 6688 RNA:lower leg skin tissue male adult (37 years) +6690 ENCFF990MDC /home/drk/tillage/datasets/human/rna/encode/ENCSR321ROU/summary/coverage.w5 768 384 0.3 sum_sqrt 6690 RNA:left renal pelvis tissue male embryo (105 days) +6691 ENCFF119SVC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR323GUF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6692 RNA:right lobe of liver tissue female adult (47 years) +6692 ENCFF119SVC- /home/drk/tillage/datasets/human/rna/encode/ENCSR323GUF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6691 RNA:right lobe of liver tissue female adult (47 years) +6693 ENCFF206GMC /home/drk/tillage/datasets/human/rna/encode/ENCSR325BJP/summary/coverage.w5 768 384 0.3 sum_sqrt 6693 RNA:K562 treated with 25 uM Galeterone for 48 hours +6694 ENCFF724LSN /home/drk/tillage/datasets/human/rna/encode/ENCSR328PVI/summary/coverage.w5 768 384 0.3 sum_sqrt 6694 RNA:renal cortex interstitium tissue male embryo (91 days) +6695 ENCFF801PRP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR329MHM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6696 RNA:HepG2 +6696 ENCFF801PRP- /home/drk/tillage/datasets/human/rna/encode/ENCSR329MHM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6695 RNA:HepG2 +6697 ENCFF575YIP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR329ZRF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6698 RNA:trophoblast tissue female embryo (40 weeks) +6698 ENCFF575YIP- /home/drk/tillage/datasets/human/rna/encode/ENCSR329ZRF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6697 RNA:trophoblast tissue female embryo (40 weeks) +6699 ENCFF643UKE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR330UMQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6700 RNA:spleen tissue male adult (37 years) +6700 ENCFF643UKE- /home/drk/tillage/datasets/human/rna/encode/ENCSR330UMQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6699 RNA:spleen tissue male adult (37 years) +6701 ENCFF197PAV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR332DBS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6702 RNA:LHCN-M2 +6702 ENCFF197PAV- /home/drk/tillage/datasets/human/rna/encode/ENCSR332DBS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6701 RNA:LHCN-M2 +6703 ENCFF956BZU /home/drk/tillage/datasets/human/rna/encode/ENCSR332MTG/summary/coverage.w5 768 384 0.3 sum_sqrt 6703 RNA:muscle of arm tissue male embryo (105 days) +6704 ENCFF080VEH /home/drk/tillage/datasets/human/rna/encode/ENCSR333FZW/summary/coverage.w5 768 384 0.3 sum_sqrt 6704 RNA:spinal cord tissue male embryo (105 days) +6705 ENCFF319AAP /home/drk/tillage/datasets/human/rna/encode/ENCSR335GET/summary/coverage.w5 768 384 0.3 sum_sqrt 6705 RNA:adrenal gland tissue male embryo (101 days) +6706 ENCFF994HKO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR336VTK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6707 RNA:T-cell female adult (33 years) +6707 ENCFF994HKO- /home/drk/tillage/datasets/human/rna/encode/ENCSR336VTK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6706 RNA:T-cell female adult (33 years) +6708 ENCFF702CEO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR338FSZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6709 RNA:chorion tissue male embryo (38 weeks) +6709 ENCFF702CEO- /home/drk/tillage/datasets/human/rna/encode/ENCSR338FSZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6708 RNA:chorion tissue male embryo (38 weeks) +6710 ENCFF010PER 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768 384 0.3 sum_sqrt 6714 RNA:mucosa of gallbladder tissue female child (16 years) +6716 ENCFF333KHL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR344MQK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6717 RNA:testis tissue male adult (54 years) +6717 ENCFF333KHL- /home/drk/tillage/datasets/human/rna/encode/ENCSR344MQK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6716 RNA:testis tissue male adult (54 years) +6718 ENCFF022QBF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR348EFG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6719 RNA:HUES64 +6719 ENCFF022QBF- /home/drk/tillage/datasets/human/rna/encode/ENCSR348EFG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6718 RNA:HUES64 +6720 ENCFF166OEV /home/drk/tillage/datasets/human/rna/encode/ENCSR348YVF/summary/coverage.w5 768 384 0.3 sum_sqrt 6720 RNA:IgD-negative memory B cell +6721 ENCFF766JPS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR351OTL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6722 RNA:esophagus squamous epithelium tissue female adult 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epithelium tissue male adult (37 years) +6728 ENCFF301XEH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR355JZC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6729 RNA:MCF-7 +6729 ENCFF301XEH- /home/drk/tillage/datasets/human/rna/encode/ENCSR355JZC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6728 RNA:MCF-7 +6730 ENCFF253SBE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR357BYU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6731 RNA:left lobe of liver tissue male adult (45 years) +6731 ENCFF253SBE- /home/drk/tillage/datasets/human/rna/encode/ENCSR357BYU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6730 RNA:left lobe of liver tissue male adult (45 years) +6732 ENCFF410ISM /home/drk/tillage/datasets/human/rna/encode/ENCSR357XTU/summary/coverage.w5 768 384 0.3 sum_sqrt 6732 RNA:natural killer cell male adult (37 years) +6733 ENCFF032EUU /home/drk/tillage/datasets/human/rna/encode/ENCSR361DRG/summary/coverage.w5 768 384 0.3 sum_sqrt 6733 RNA:fibroblast of skin of abdomen male embryo (97 days) +6734 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384 0.3 sum_sqrt 6756 RNA:K562 treated with 5 uM MB-3 for 48 hours +6757 ENCFF527SQU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR379DEC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6758 RNA:GM23338 +6758 ENCFF527SQU- /home/drk/tillage/datasets/human/rna/encode/ENCSR379DEC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6757 RNA:GM23338 +6759 ENCFF205VDK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR379YAE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6760 RNA:cardiac muscle cell originated from RUES2 +6760 ENCFF205VDK- /home/drk/tillage/datasets/human/rna/encode/ENCSR379YAE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6759 RNA:cardiac muscle cell originated from RUES2 +6761 ENCFF358XLV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR381OTM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6762 RNA:HFFc6 +6762 ENCFF358XLV- /home/drk/tillage/datasets/human/rna/encode/ENCSR381OTM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6761 RNA:HFFc6 +6763 ENCFF081XYH+ 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years) +6785 ENCFF493OET- /home/drk/tillage/datasets/human/rna/encode/ENCSR406SAW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6784 RNA:upper lobe of left lung tissue female adult (53 years) +6786 ENCFF309YCI /home/drk/tillage/datasets/human/rna/encode/ENCSR406YML/summary/coverage.w5 768 384 0.3 sum_sqrt 6786 RNA:muscle of arm tissue male embryo (91 days) +6787 ENCFF407ZDM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR409JSP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6788 RNA:peripheral blood mononuclear cell male adult (39 years) +6788 ENCFF407ZDM- /home/drk/tillage/datasets/human/rna/encode/ENCSR409JSP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6787 RNA:peripheral blood mononuclear cell male adult (39 years) +6789 ENCFF251CIC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR409UYW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6790 RNA:activated naive CD8-positive, alpha-beta T cell male adult (30 years) +6790 ENCFF251CIC- /home/drk/tillage/datasets/human/rna/encode/ENCSR409UYW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6789 RNA:activated naive CD8-positive, alpha-beta T cell male adult (30 years) +6791 ENCFF563MLL /home/drk/tillage/datasets/human/rna/encode/ENCSR410DUZ/summary/coverage.w5 768 384 0.3 sum_sqrt 6791 RNA:left renal pelvis tissue male embryo (120 days) +6792 ENCFF808KRP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR410MSS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6793 RNA:left lung tissue female child (16 years) +6793 ENCFF808KRP- /home/drk/tillage/datasets/human/rna/encode/ENCSR410MSS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6792 RNA:left lung tissue female child (16 years) +6794 ENCFF515TIF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR411MUF/summary/coverage+.w5 768 384 0.3 sum_sqrt 6795 RNA:CD4-positive, alpha-beta T cell male adult (20 years) +6795 ENCFF515TIF- /home/drk/tillage/datasets/human/rna/encode/ENCSR411MUF/summary/coverage-.w5 768 384 0.3 sum_sqrt 6794 RNA:CD4-positive, alpha-beta T cell male adult (20 years) +6796 ENCFF251HQX /home/drk/tillage/datasets/human/rna/encode/ENCSR413LXW/summary/coverage.w5 768 384 0.3 sum_sqrt 6796 RNA:left renal cortex interstitium tissue male embryo (105 days) +6797 ENCFF092QIW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR413QAL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6798 RNA:osteocyte +6798 ENCFF092QIW- /home/drk/tillage/datasets/human/rna/encode/ENCSR413QAL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6797 RNA:osteocyte +6799 ENCFF474MDU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR415SXI/summary/coverage+.w5 768 384 0.3 sum_sqrt 6800 RNA:activated CD8-positive, alpha-beta memory T cell male adult (30 years) +6800 ENCFF474MDU- /home/drk/tillage/datasets/human/rna/encode/ENCSR415SXI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6799 RNA:activated CD8-positive, alpha-beta memory T cell male adult (30 years) +6801 ENCFF743FLM 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768 384 0.3 sum_sqrt 6837 RNA:heart right ventricle tissue male child (3 years) +6837 ENCFF841CUM- /home/drk/tillage/datasets/human/rna/encode/ENCSR439SPU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6836 RNA:heart right ventricle tissue male child (3 years) +6838 ENCFF485JGG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR444WHQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6839 RNA:skeletal muscle myoblast +6839 ENCFF485JGG- /home/drk/tillage/datasets/human/rna/encode/ENCSR444WHQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6838 RNA:skeletal muscle myoblast +6840 ENCFF121WXQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR445DAC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6841 RNA:chorionic villus tissue male embryo (38 weeks) +6841 ENCFF121WXQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR445DAC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6840 RNA:chorionic villus tissue male embryo (38 weeks) +6842 ENCFF030XBO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR446LDS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6843 RNA:CD8-positive, alpha-beta memory T cell male adult (30 years) +6843 ENCFF030XBO- /home/drk/tillage/datasets/human/rna/encode/ENCSR446LDS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6842 RNA:CD8-positive, alpha-beta memory T cell male adult (30 years) +6844 ENCFF224GPU /home/drk/tillage/datasets/human/rna/encode/ENCSR446RKD/summary/coverage.w5 768 384 0.3 sum_sqrt 6844 RNA:small intestine tissue male embryo (91 days) +6845 ENCFF846ZCR /home/drk/tillage/datasets/human/rna/encode/ENCSR447IJE/summary/coverage.w5 768 384 0.3 sum_sqrt 6845 RNA:muscle of leg tissue male embryo (101 days) +6846 ENCFF327YQU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR448BTT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6847 RNA:lower lobe of left lung tissue male adult (60 years) +6847 ENCFF327YQU- /home/drk/tillage/datasets/human/rna/encode/ENCSR448BTT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6846 RNA:lower lobe of left lung tissue male adult (60 years) +6848 ENCFF214DTC+ 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/home/drk/tillage/datasets/human/rna/encode/ENCSR452VLO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6861 RNA:foreskin keratinocyte male newborn +6861 ENCFF283IQC- /home/drk/tillage/datasets/human/rna/encode/ENCSR452VLO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6860 RNA:foreskin keratinocyte male newborn +6862 ENCFF263KEJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR457ENP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6863 RNA:right atrium auricular region tissue female adult (51 years) +6863 ENCFF263KEJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR457ENP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6862 RNA:right atrium auricular region tissue female adult (51 years) +6864 ENCFF286TKQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR458FZP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6865 RNA:activated naive CD4-positive, alpha-beta T cell male adult (43 years) +6865 ENCFF286TKQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR458FZP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6864 RNA:activated naive CD4-positive, alpha-beta T cell male adult (43 years) +6866 ENCFF318EJE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR460YCS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6867 RNA:lower leg skin tissue male adult (54 years) +6867 ENCFF318EJE- /home/drk/tillage/datasets/human/rna/encode/ENCSR460YCS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6866 RNA:lower leg skin tissue male adult (54 years) +6868 ENCFF223MUU /home/drk/tillage/datasets/human/rna/encode/ENCSR463JBR/summary/coverage.w5 768 384 0.3 sum_sqrt 6868 RNA:CD4-positive, alpha-beta T cell male adult (37 years) +6869 ENCFF992XOR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR464VSR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6870 RNA:placenta tissue male embryo +6870 ENCFF992XOR- /home/drk/tillage/datasets/human/rna/encode/ENCSR464VSR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6869 RNA:placenta tissue male embryo +6871 ENCFF064BKZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR466XAR/summary/coverage+.w5 768 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/home/drk/tillage/datasets/human/rna/encode/ENCSR470JHE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6877 RNA:cerebellum tissue male embryo (20 weeks) +6879 ENCFF561TMR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR471RUK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6880 RNA:stomach tissue male adult (37 years) +6880 ENCFF561TMR- /home/drk/tillage/datasets/human/rna/encode/ENCSR471RUK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6879 RNA:stomach tissue male adult (37 years) +6881 ENCFF911JBW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR472PBS/summary/coverage+.w5 768 384 0.3 sum_sqrt 6882 RNA:endodermal cell originated from HUES64 +6882 ENCFF911JBW- /home/drk/tillage/datasets/human/rna/encode/ENCSR472PBS/summary/coverage-.w5 768 384 0.3 sum_sqrt 6881 RNA:endodermal cell originated from HUES64 +6883 ENCFF291GNY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR473XAP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6884 RNA:naive thymus-derived CD8-positive, alpha-beta T cell male adult (30 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ENCFF697OAU- /home/drk/tillage/datasets/human/rna/encode/ENCSR484WZL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6894 RNA:placenta tissue embryo +6896 ENCFF263ZRO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR485WBR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6897 RNA:gastroesophageal sphincter tissue male adult (54 years) +6897 ENCFF263ZRO- /home/drk/tillage/datasets/human/rna/encode/ENCSR485WBR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6896 RNA:gastroesophageal sphincter tissue male adult (54 years) +6898 ENCFF181QTI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR490SQH/summary/coverage+.w5 768 384 0.3 sum_sqrt 6899 RNA:H7 +6899 ENCFF181QTI- /home/drk/tillage/datasets/human/rna/encode/ENCSR490SQH/summary/coverage-.w5 768 384 0.3 sum_sqrt 6898 RNA:H7 +6900 ENCFF470HTA /home/drk/tillage/datasets/human/rna/encode/ENCSR491XNW/summary/coverage.w5 768 384 0.3 sum_sqrt 6900 RNA:with multiple sclerosis; CD8-positive, alpha-beta memory T cell +6901 ENCFF952UWM /home/drk/tillage/datasets/human/rna/encode/ENCSR492KRY/summary/coverage.w5 768 384 0.3 sum_sqrt 6901 RNA:K562 treated with 10 nM Chaetocin for 4 hours +6902 ENCFF535TIX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR495HDM/summary/coverage+.w5 768 384 0.3 sum_sqrt 6903 RNA:prostate gland tissue male adult (37 years) +6903 ENCFF535TIX- /home/drk/tillage/datasets/human/rna/encode/ENCSR495HDM/summary/coverage-.w5 768 384 0.3 sum_sqrt 6902 RNA:prostate gland tissue male adult (37 years) +6904 ENCFF143EWZ /home/drk/tillage/datasets/human/rna/encode/ENCSR495UXA/summary/coverage.w5 768 384 0.3 sum_sqrt 6904 RNA:kidney tissue female embryo (108 days) +6905 ENCFF089GUP /home/drk/tillage/datasets/human/rna/encode/ENCSR499NEL/summary/coverage.w5 768 384 0.3 sum_sqrt 6905 RNA:left lung tissue female embryo (105 days) +6906 ENCFF849BKN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR500JSJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6907 RNA:upper lobe of left lung tissue male adult (60 years) 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muscle tissue female adult (30 years) +6913 ENCFF754ZRA- /home/drk/tillage/datasets/human/rna/encode/ENCSR502OTI/summary/coverage-.w5 768 384 0.3 sum_sqrt 6912 RNA:psoas muscle tissue female adult (30 years) +6914 ENCFF560FVE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR504NIU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6915 RNA:subcutaneous adipose tissue tissue female adult (53 years) +6915 ENCFF560FVE- /home/drk/tillage/datasets/human/rna/encode/ENCSR504NIU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6914 RNA:subcutaneous adipose tissue tissue female adult (53 years) +6916 ENCFF672AXQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR504QMK/summary/coverage+.w5 768 384 0.3 sum_sqrt 6917 RNA:right lobe of liver tissue female adult (53 years) +6917 ENCFF672AXQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR504QMK/summary/coverage-.w5 768 384 0.3 sum_sqrt 6916 RNA:right lobe of liver tissue female adult (53 years) +6918 ENCFF280YRS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR504VXC/summary/coverage+.w5 768 384 0.3 sum_sqrt 6919 RNA:A375 +6919 ENCFF280YRS- /home/drk/tillage/datasets/human/rna/encode/ENCSR504VXC/summary/coverage-.w5 768 384 0.3 sum_sqrt 6918 RNA:A375 +6920 ENCFF833QMT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR510MIA/summary/coverage+.w5 768 384 0.3 sum_sqrt 6921 RNA:esophagus squamous epithelium tissue female adult (51 years) +6921 ENCFF833QMT- /home/drk/tillage/datasets/human/rna/encode/ENCSR510MIA/summary/coverage-.w5 768 384 0.3 sum_sqrt 6920 RNA:esophagus squamous epithelium tissue female adult (51 years) +6922 ENCFF089SDX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR510PSL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6923 RNA:spleen tissue female adult (30 years) +6923 ENCFF089SDX- /home/drk/tillage/datasets/human/rna/encode/ENCSR510PSL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6922 RNA:spleen tissue female adult (30 years) +6924 ENCFF693XEN 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(120 days) +6930 ENCFF344YVW /home/drk/tillage/datasets/human/rna/encode/ENCSR518BSQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6930 RNA:K562 treated with 10 uM Crizotinib for 4 hours +6931 ENCFF670XJQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR518XRJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6932 RNA:endocrine pancreas tissue male adult (45 years) +6932 ENCFF670XJQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR518XRJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6931 RNA:endocrine pancreas tissue male adult (45 years) +6933 ENCFF027CXS /home/drk/tillage/datasets/human/rna/encode/ENCSR522XTV/summary/coverage.w5 768 384 0.3 sum_sqrt 6933 RNA:muscle of back tissue male embryo (101 days) +6934 ENCFF849FLT /home/drk/tillage/datasets/human/rna/encode/ENCSR523EDD/summary/coverage.w5 768 384 0.3 sum_sqrt 6934 RNA:small intestine tissue female embryo (120 days) +6935 ENCFF901ATL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR523RGW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6936 RNA:pancreas tissue female adult (47 years) +6936 ENCFF901ATL- /home/drk/tillage/datasets/human/rna/encode/ENCSR523RGW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6935 RNA:pancreas tissue female adult (47 years) +6937 ENCFF069OIK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR528ZKN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6938 RNA:gastroesophageal sphincter tissue male adult (37 years) +6938 ENCFF069OIK- /home/drk/tillage/datasets/human/rna/encode/ENCSR528ZKN/summary/coverage-.w5 768 384 0.3 sum_sqrt 6937 RNA:gastroesophageal sphincter tissue male adult (37 years) +6939 ENCFF113MGH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR530NHO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6940 RNA:K562 nuclear fraction +6940 ENCFF113MGH- /home/drk/tillage/datasets/human/rna/encode/ENCSR530NHO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6939 RNA:K562 nuclear fraction +6941 ENCFF007LJG /home/drk/tillage/datasets/human/rna/encode/ENCSR531RKI/summary/coverage.w5 768 384 0.3 sum_sqrt 6941 RNA:muscle of trunk tissue female embryo (120 days) +6942 ENCFF101SYV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR532LJV/summary/coverage+.w5 768 384 0.3 sum_sqrt 6943 RNA:thyroid gland tissue male adult (37 years) +6943 ENCFF101SYV- /home/drk/tillage/datasets/human/rna/encode/ENCSR532LJV/summary/coverage-.w5 768 384 0.3 sum_sqrt 6942 RNA:thyroid gland tissue male adult (37 years) +6944 ENCFF646ZZQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR533TOW/summary/coverage+.w5 768 384 0.3 sum_sqrt 6945 RNA:activated CD8-positive, alpha-beta T cell male adult (21 years) treated with anti-CD3 and anti-CD28 coated beads +6945 ENCFF646ZZQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR533TOW/summary/coverage-.w5 768 384 0.3 sum_sqrt 6944 RNA:activated CD8-positive, alpha-beta T cell male adult (21 years) treated with anti-CD3 and anti-CD28 coated beads +6946 ENCFF298CPL /home/drk/tillage/datasets/human/rna/encode/ENCSR534JVH/summary/coverage.w5 768 384 0.3 sum_sqrt 6946 RNA:small intestine tissue female embryo (98 days) +6947 ENCFF636BRP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR534UXT/summary/coverage+.w5 768 384 0.3 sum_sqrt 6948 RNA:amnion tissue female embryo (40 weeks) +6948 ENCFF636BRP- /home/drk/tillage/datasets/human/rna/encode/ENCSR534UXT/summary/coverage-.w5 768 384 0.3 sum_sqrt 6947 RNA:amnion tissue female embryo (40 weeks) +6949 ENCFF790DEA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR535VTR/summary/coverage+.w5 768 384 0.3 sum_sqrt 6950 RNA:HT1080 +6950 ENCFF790DEA- /home/drk/tillage/datasets/human/rna/encode/ENCSR535VTR/summary/coverage-.w5 768 384 0.3 sum_sqrt 6949 RNA:HT1080 +6951 ENCFF709BGZ /home/drk/tillage/datasets/human/rna/encode/ENCSR535YOP/summary/coverage.w5 768 384 0.3 sum_sqrt 6951 RNA:with multiple sclerosis; IgD-negative memory B cell +6952 ENCFF257QQB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR537BCG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6953 RNA:H1 +6953 ENCFF257QQB- /home/drk/tillage/datasets/human/rna/encode/ENCSR537BCG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6952 RNA:H1 +6954 ENCFF982JPV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR538FRP/summary/coverage+.w5 768 384 0.3 sum_sqrt 6955 RNA:activated CD8-positive, alpha-beta memory T cell male adult (30 years) +6955 ENCFF982JPV- /home/drk/tillage/datasets/human/rna/encode/ENCSR538FRP/summary/coverage-.w5 768 384 0.3 sum_sqrt 6954 RNA:activated CD8-positive, alpha-beta memory T cell male adult (30 years) +6956 ENCFF808EKP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR541TIG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6957 RNA:HepG2 membrane fraction +6957 ENCFF808EKP- /home/drk/tillage/datasets/human/rna/encode/ENCSR541TIG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6956 RNA:HepG2 membrane fraction +6958 ENCFF595DZY /home/drk/tillage/datasets/human/rna/encode/ENCSR542OHE/summary/coverage.w5 768 384 0.3 sum_sqrt 6958 RNA:spinal cord tissue female embryo (113 days) +6959 ENCFF876MLB /home/drk/tillage/datasets/human/rna/encode/ENCSR543TQW/summary/coverage.w5 768 384 0.3 sum_sqrt 6959 RNA:right renal pelvis tissue male embryo (120 days) +6960 ENCFF684FER+ /home/drk/tillage/datasets/human/rna/encode/ENCSR544SAU/summary/coverage+.w5 768 384 0.3 sum_sqrt 6961 RNA:Peyer's patch tissue female adult (53 years) +6961 ENCFF684FER- /home/drk/tillage/datasets/human/rna/encode/ENCSR544SAU/summary/coverage-.w5 768 384 0.3 sum_sqrt 6960 RNA:Peyer's patch tissue female adult (53 years) +6962 ENCFF089BOJ /home/drk/tillage/datasets/human/rna/encode/ENCSR545MEZ/summary/coverage.w5 768 384 0.3 sum_sqrt 6962 RNA:CD4-positive, alpha-beta T cell male adult (21 years) +6963 ENCFF844CIZ /home/drk/tillage/datasets/human/rna/encode/ENCSR545WAC/summary/coverage.w5 768 384 0.3 sum_sqrt 6963 RNA:muscle of leg tissue male embryo (97 days) +6964 ENCFF713ZMW /home/drk/tillage/datasets/human/rna/encode/ENCSR547TNE/summary/coverage.w5 768 384 0.3 sum_sqrt 6964 RNA:muscle of arm tissue male embryo (96 days) +6965 ENCFF728QLF /home/drk/tillage/datasets/human/rna/encode/ENCSR549DVY/summary/coverage.w5 768 384 0.3 sum_sqrt 6965 RNA:stomach tissue female embryo (108 days) +6966 ENCFF410QZX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR551NII/summary/coverage+.w5 768 384 0.3 sum_sqrt 6967 RNA:lower leg skin tissue female adult (51 years) +6967 ENCFF410QZX- /home/drk/tillage/datasets/human/rna/encode/ENCSR551NII/summary/coverage-.w5 768 384 0.3 sum_sqrt 6966 RNA:lower leg skin tissue female adult (51 years) +6968 ENCFF150UWD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR552EGO/summary/coverage+.w5 768 384 0.3 sum_sqrt 6969 RNA:HeLa-S3 +6969 ENCFF150UWD- /home/drk/tillage/datasets/human/rna/encode/ENCSR552EGO/summary/coverage-.w5 768 384 0.3 sum_sqrt 6968 RNA:HeLa-S3 +6970 ENCFF707WTD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR552RFJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 6971 RNA:stimulated activated CD8-positive, alpha-beta T cell male adult (21 years) treated with 10 ng/mL Interleukin-2, anti-CD3 and anti-CD28 coated beads +6971 ENCFF707WTD- /home/drk/tillage/datasets/human/rna/encode/ENCSR552RFJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 6970 RNA:stimulated activated CD8-positive, alpha-beta T cell male adult (21 years) treated with 10 ng/mL Interleukin-2, anti-CD3 and anti-CD28 coated beads +6972 ENCFF146DMX /home/drk/tillage/datasets/human/rna/encode/ENCSR552YAE/summary/coverage.w5 768 384 0.3 sum_sqrt 6972 RNA:right renal pelvis tissue male embryo (105 days) +6973 ENCFF085JXX /home/drk/tillage/datasets/human/rna/encode/ENCSR554KBK/summary/coverage.w5 768 384 0.3 sum_sqrt 6973 RNA:right lung tissue female embryo (108 days) +6974 ENCFF489SFV /home/drk/tillage/datasets/human/rna/encode/ENCSR555BCP/summary/coverage.w5 768 384 0.3 sum_sqrt 6974 RNA:adrenal gland tissue embryo (96 days) +6975 ENCFF866JMO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR557PFL/summary/coverage+.w5 768 384 0.3 sum_sqrt 6976 RNA:amnion tissue embryo (16 weeks) +6976 ENCFF866JMO- /home/drk/tillage/datasets/human/rna/encode/ENCSR557PFL/summary/coverage-.w5 768 384 0.3 sum_sqrt 6975 RNA:amnion tissue embryo (16 weeks) +6977 ENCFF274TDF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR558SEE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6978 RNA:A673 +6978 ENCFF274TDF- /home/drk/tillage/datasets/human/rna/encode/ENCSR558SEE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6977 RNA:A673 +6979 ENCFF565XVW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR559HWG/summary/coverage+.w5 768 384 0.3 sum_sqrt 6980 RNA:endodermal cell originated from H1 +6980 ENCFF565XVW- /home/drk/tillage/datasets/human/rna/encode/ENCSR559HWG/summary/coverage-.w5 768 384 0.3 sum_sqrt 6979 RNA:endodermal cell originated from H1 +6981 ENCFF744BTD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR560IFD/summary/coverage+.w5 768 384 0.3 sum_sqrt 6982 RNA:chorionic villus tissue male embryo (16 weeks) +6982 ENCFF744BTD- /home/drk/tillage/datasets/human/rna/encode/ENCSR560IFD/summary/coverage-.w5 768 384 0.3 sum_sqrt 6981 RNA:chorionic villus tissue male embryo (16 weeks) +6983 ENCFF488KNY /home/drk/tillage/datasets/human/rna/encode/ENCSR560MDQ/summary/coverage.w5 768 384 0.3 sum_sqrt 6983 RNA:right lung tissue female embryo (105 days) +6984 ENCFF917RKL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR561FEE/summary/coverage+.w5 768 384 0.3 sum_sqrt 6985 RNA:HepG2 +6985 ENCFF917RKL- /home/drk/tillage/datasets/human/rna/encode/ENCSR561FEE/summary/coverage-.w5 768 384 0.3 sum_sqrt 6984 RNA:HepG2 +6986 ENCFF951UGT /home/drk/tillage/datasets/human/rna/encode/ENCSR561WEX/summary/coverage.w5 768 384 0.3 sum_sqrt 6986 RNA:muscle of leg tissue male embryo (97 days) +6987 ENCFF104NDB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR562BUN/summary/coverage+.w5 768 384 0.3 sum_sqrt 6988 RNA:middle frontal area 46 tissue female adult (90 or above years) +6988 ENCFF104NDB- 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/home/drk/tillage/datasets/human/rna/encode/ENCSR569JKX/summary/coverage+.w5 768 384 0.3 sum_sqrt 6995 RNA:SK-N-DZ cytosolic fraction +6995 ENCFF218MMR- /home/drk/tillage/datasets/human/rna/encode/ENCSR569JKX/summary/coverage-.w5 768 384 0.3 sum_sqrt 6994 RNA:SK-N-DZ cytosolic fraction +6996 ENCFF898IHN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR571BML/summary/coverage+.w5 768 384 0.3 sum_sqrt 6997 RNA:pancreas tissue female adult (30 years) +6997 ENCFF898IHN- /home/drk/tillage/datasets/human/rna/encode/ENCSR571BML/summary/coverage-.w5 768 384 0.3 sum_sqrt 6996 RNA:pancreas tissue female adult (30 years) +6998 ENCFF212QRL /home/drk/tillage/datasets/human/rna/encode/ENCSR571IUW/summary/coverage.w5 768 384 0.3 sum_sqrt 6998 RNA:stomach tissue female embryo (110 days) +6999 ENCFF025THJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR571RXE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7000 RNA:right atrium auricular region tissue female adult (53 years) +7000 ENCFF025THJ- 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/home/drk/tillage/datasets/human/rna/encode/ENCSR584JXD/summary/coverage+.w5 768 384 0.3 sum_sqrt 7013 RNA:Caki2 +7013 ENCFF591XND- /home/drk/tillage/datasets/human/rna/encode/ENCSR584JXD/summary/coverage-.w5 768 384 0.3 sum_sqrt 7012 RNA:Caki2 +7014 ENCFF201RLE /home/drk/tillage/datasets/human/rna/encode/ENCSR585DJN/summary/coverage.w5 768 384 0.3 sum_sqrt 7014 RNA:with multiple sclerosis; naive thymus-derived CD8-positive, alpha-beta T cell +7015 ENCFF304TWT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR586SEE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7016 RNA:NCI-H460 cytosolic fraction +7016 ENCFF304TWT- /home/drk/tillage/datasets/human/rna/encode/ENCSR586SEE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7015 RNA:NCI-H460 cytosolic fraction +7017 ENCFF731FYT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR586SYA/summary/coverage+.w5 768 384 0.3 sum_sqrt 7018 RNA:body of pancreas tissue female adult (53 years) +7018 ENCFF731FYT- 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sum_sqrt 7034 RNA:naive thymus-derived CD4-positive, alpha-beta T cell +7035 ENCFF455CDH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR596KAH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7036 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (90 or above years) +7036 ENCFF455CDH- /home/drk/tillage/datasets/human/rna/encode/ENCSR596KAH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7035 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (90 or above years) +7037 ENCFF297NQG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR598KJX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7038 RNA:adrenal gland tissue male adult (34 years) +7038 ENCFF297NQG- /home/drk/tillage/datasets/human/rna/encode/ENCSR598KJX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7037 RNA:adrenal gland tissue male adult (34 years) +7039 ENCFF065NBH /home/drk/tillage/datasets/human/rna/encode/ENCSR601DZY/summary/coverage.w5 768 384 0.3 sum_sqrt 7039 RNA:K562 treated with 1% DMSO for 12 hours +7040 ENCFF007ZBY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR609NZM/summary/coverage+.w5 768 384 0.3 sum_sqrt 7041 RNA:gastrocnemius medialis tissue female adult (51 years) +7041 ENCFF007ZBY- /home/drk/tillage/datasets/human/rna/encode/ENCSR609NZM/summary/coverage-.w5 768 384 0.3 sum_sqrt 7040 RNA:gastrocnemius medialis tissue female adult (51 years) +7042 ENCFF097CWH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR612HYR/summary/coverage+.w5 768 384 0.3 sum_sqrt 7043 RNA:small intestine tissue female adult (30 years) +7043 ENCFF097CWH- /home/drk/tillage/datasets/human/rna/encode/ENCSR612HYR/summary/coverage-.w5 768 384 0.3 sum_sqrt 7042 RNA:small intestine tissue female adult (30 years) +7044 ENCFF585HTZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR615EEK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7045 RNA:K562 +7045 ENCFF585HTZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR615EEK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7044 RNA:K562 +7046 ENCFF458QQU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR618IQY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7047 RNA:small intestine tissue male child (3 years) +7047 ENCFF458QQU- /home/drk/tillage/datasets/human/rna/encode/ENCSR618IQY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7046 RNA:small intestine tissue male child (3 years) +7048 ENCFF973BSN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR620LQN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7049 RNA:esophagus muscularis mucosa tissue female adult (51 years) +7049 ENCFF973BSN- /home/drk/tillage/datasets/human/rna/encode/ENCSR620LQN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7048 RNA:esophagus muscularis mucosa tissue female adult (51 years) +7050 ENCFF383RPD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR620NSN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7051 RNA:bronchus fibroblast of lung +7051 ENCFF383RPD- /home/drk/tillage/datasets/human/rna/encode/ENCSR620NSN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7050 RNA:bronchus fibroblast of lung +7052 ENCFF824QUG /home/drk/tillage/datasets/human/rna/encode/ENCSR620ZNQ/summary/coverage.w5 768 384 0.3 sum_sqrt 7052 RNA:muscle of arm tissue female embryo (105 days) +7053 ENCFF592XZA /home/drk/tillage/datasets/human/rna/encode/ENCSR621FYE/summary/coverage.w5 768 384 0.3 sum_sqrt 7053 RNA:small intestine tissue male embryo (115 days) +7054 ENCFF733JPK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR621PZI/summary/coverage+.w5 768 384 0.3 sum_sqrt 7055 RNA:spleen tissue female adult (41 years) +7055 ENCFF733JPK- /home/drk/tillage/datasets/human/rna/encode/ENCSR621PZI/summary/coverage-.w5 768 384 0.3 sum_sqrt 7054 RNA:spleen tissue female adult (41 years) +7056 ENCFF808SDN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR622PIH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7057 RNA:right cardiac atrium tissue female adult (59 years) +7057 ENCFF808SDN- /home/drk/tillage/datasets/human/rna/encode/ENCSR622PIH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7056 RNA:right cardiac atrium tissue female adult (59 years) +7058 ENCFF086IIB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR625QJI/summary/coverage+.w5 768 384 0.3 sum_sqrt 7059 RNA:NCI-H460 nuclear fraction +7059 ENCFF086IIB- /home/drk/tillage/datasets/human/rna/encode/ENCSR625QJI/summary/coverage-.w5 768 384 0.3 sum_sqrt 7058 RNA:NCI-H460 nuclear fraction +7060 ENCFF091AGW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR629VMZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7061 RNA:pancreas tissue male adult (34 years) +7061 ENCFF091AGW- /home/drk/tillage/datasets/human/rna/encode/ENCSR629VMZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7060 RNA:pancreas tissue male adult (34 years) +7062 ENCFF672VYQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR630VJN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7063 RNA:transverse colon tissue male adult (54 years) +7063 ENCFF672VYQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR630VJN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7062 RNA:transverse colon tissue male adult (54 years) +7064 ENCFF983RQU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR631FXT/summary/coverage+.w5 768 384 0.3 sum_sqrt 7065 RNA:T-cell male adult (38 years) +7065 ENCFF983RQU- /home/drk/tillage/datasets/human/rna/encode/ENCSR631FXT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7064 RNA:T-cell male adult (38 years) +7066 ENCFF296HLN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR631NUQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7067 RNA:sciatic nerve tissue female adult (41 years) +7067 ENCFF296HLN- /home/drk/tillage/datasets/human/rna/encode/ENCSR631NUQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7066 RNA:sciatic nerve tissue female adult (41 years) +7068 ENCFF482BDQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR634JQK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7069 RNA:middle frontal area 46 tissue female adult (90 or above years) +7069 ENCFF482BDQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR634JQK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7068 RNA:middle frontal area 46 tissue female adult (90 or above years) +7070 ENCFF814YUZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR634LOX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7071 RNA:foreskin melanocyte male newborn +7071 ENCFF814YUZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR634LOX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7070 RNA:foreskin melanocyte male newborn +7072 ENCFF045ZHZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR635GTY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7073 RNA:heart tissue female adult (30 years) +7073 ENCFF045ZHZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR635GTY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7072 RNA:heart tissue female adult (30 years) +7074 ENCFF275DKR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR636LEU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7075 RNA:HFFc6 +7075 ENCFF275DKR- /home/drk/tillage/datasets/human/rna/encode/ENCSR636LEU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7074 RNA:HFFc6 +7076 ENCFF365LTY /home/drk/tillage/datasets/human/rna/encode/ENCSR637GBV/summary/coverage.w5 768 384 0.3 sum_sqrt 7076 RNA:fibroblast of skin of back male embryo (97 days) +7077 ENCFF544ZDA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR637VLS/summary/coverage+.w5 768 384 0.3 sum_sqrt 7078 RNA:K562 +7078 ENCFF544ZDA- /home/drk/tillage/datasets/human/rna/encode/ENCSR637VLS/summary/coverage-.w5 768 384 0.3 sum_sqrt 7077 RNA:K562 +7079 ENCFF848ZVQ /home/drk/tillage/datasets/human/rna/encode/ENCSR638OAH/summary/coverage.w5 768 384 0.3 sum_sqrt 7079 RNA:with multiple sclerosis; CD14-positive monocyte +7080 ENCFF368FFC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR643QIZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7081 RNA:H1 +7081 ENCFF368FFC- /home/drk/tillage/datasets/human/rna/encode/ENCSR643QIZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7080 RNA:H1 +7082 ENCFF889JRS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR645TCG/summary/coverage+.w5 768 384 0.3 sum_sqrt 7083 RNA:omental fat pad tissue female adult (53 years) +7083 ENCFF889JRS- /home/drk/tillage/datasets/human/rna/encode/ENCSR645TCG/summary/coverage-.w5 768 384 0.3 sum_sqrt 7082 RNA:omental fat pad tissue female adult (53 years) +7084 ENCFF857GII+ /home/drk/tillage/datasets/human/rna/encode/ENCSR648JOK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7085 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (90 or above years) +7085 ENCFF857GII- /home/drk/tillage/datasets/human/rna/encode/ENCSR648JOK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7084 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (90 or above years) +7086 ENCFF702XYL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR648KDM/summary/coverage+.w5 768 384 0.3 sum_sqrt 7087 RNA:PC-3 +7087 ENCFF702XYL- /home/drk/tillage/datasets/human/rna/encode/ENCSR648KDM/summary/coverage-.w5 768 384 0.3 sum_sqrt 7086 RNA:PC-3 +7088 ENCFF304ZAM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR648OSR/summary/coverage+.w5 768 384 0.3 sum_sqrt 7089 RNA:tibial nerve tissue male adult (54 years) +7089 ENCFF304ZAM- /home/drk/tillage/datasets/human/rna/encode/ENCSR648OSR/summary/coverage-.w5 768 384 0.3 sum_sqrt 7088 RNA:tibial nerve tissue male adult (54 years) +7090 ENCFF196UHI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR648YUM/summary/coverage+.w5 768 384 0.3 sum_sqrt 7091 RNA:placenta tissue female embryo +7091 ENCFF196UHI- /home/drk/tillage/datasets/human/rna/encode/ENCSR648YUM/summary/coverage-.w5 768 384 0.3 sum_sqrt 7090 RNA:placenta tissue female embryo +7092 ENCFF519CVR /home/drk/tillage/datasets/human/rna/encode/ENCSR652AWW/summary/coverage.w5 768 384 0.3 sum_sqrt 7092 RNA:muscle of back tissue male embryo (105 days) +7093 ENCFF185FBE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR652PHZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7094 RNA:left cardiac atrium tissue female adult (59 years) +7094 ENCFF185FBE- /home/drk/tillage/datasets/human/rna/encode/ENCSR652PHZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7093 RNA:left cardiac atrium tissue female adult (59 years) +7095 ENCFF125TVD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR653DFZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7096 RNA:G401 +7096 ENCFF125TVD- /home/drk/tillage/datasets/human/rna/encode/ENCSR653DFZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7095 RNA:G401 +7097 ENCFF844TIV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR653ZJF/summary/coverage+.w5 768 384 0.312421875 sum_sqrt 7098 RNA:transverse colon tissue male adult (37 years) +7098 ENCFF844TIV- /home/drk/tillage/datasets/human/rna/encode/ENCSR653ZJF/summary/coverage-.w5 768 384 0.312421875 sum_sqrt 7097 RNA:transverse colon tissue male adult (37 years) +7099 ENCFF443EQZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR654UPQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7100 RNA:endothelial cell of umbilical vein newborn +7100 ENCFF443EQZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR654UPQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7099 RNA:endothelial cell of umbilical vein newborn +7101 ENCFF893OBW /home/drk/tillage/datasets/human/rna/encode/ENCSR655XQF/summary/coverage.w5 768 384 0.3 sum_sqrt 7101 RNA:fibroblast of skin of back male embryo (97 days) +7102 ENCFF168WRO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR663IOE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7103 RNA:spleen tissue male child (3 years) +7103 ENCFF168WRO- /home/drk/tillage/datasets/human/rna/encode/ENCSR663IOE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7102 RNA:spleen tissue male child (3 years) +7104 ENCFF807FQZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR663WGC/summary/coverage+.w5 768 384 0.3 sum_sqrt 7105 RNA:mesenchymal stem cell originated from H1 +7105 ENCFF807FQZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR663WGC/summary/coverage-.w5 768 384 0.3 sum_sqrt 7104 RNA:mesenchymal stem cell originated from H1 +7106 ENCFF497DVM /home/drk/tillage/datasets/human/rna/encode/ENCSR667OPL/summary/coverage.w5 768 384 0.3 sum_sqrt 7106 RNA:CD4-positive, CD25-positive, alpha-beta regulatory T cell +7107 ENCFF492KPL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR669KQU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7108 RNA:SK-MEL-5 +7108 ENCFF492KPL- /home/drk/tillage/datasets/human/rna/encode/ENCSR669KQU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7107 RNA:SK-MEL-5 +7109 ENCFF190ZWO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR670WQY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7110 RNA:H1 +7110 ENCFF190ZWO- /home/drk/tillage/datasets/human/rna/encode/ENCSR670WQY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7109 RNA:H1 +7111 ENCFF784RHW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR671IYC/summary/coverage+.w5 768 384 0.3 sum_sqrt 7112 RNA:body of pancreas tissue female adult (51 years) +7112 ENCFF784RHW- /home/drk/tillage/datasets/human/rna/encode/ENCSR671IYC/summary/coverage-.w5 768 384 0.3 sum_sqrt 7111 RNA:body of pancreas tissue female adult (51 years) +7113 ENCFF402SEK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR671WMH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7114 RNA:subcutaneous adipose tissue tissue male adult (54 years) +7114 ENCFF402SEK- /home/drk/tillage/datasets/human/rna/encode/ENCSR671WMH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7113 RNA:subcutaneous adipose tissue tissue male adult (54 years) +7115 ENCFF851BGA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR672JUF/summary/coverage+.w5 768 384 0.3 sum_sqrt 7116 RNA:foreskin keratinocyte male newborn +7116 ENCFF851BGA- /home/drk/tillage/datasets/human/rna/encode/ENCSR672JUF/summary/coverage-.w5 768 384 0.3 sum_sqrt 7115 RNA:foreskin keratinocyte male newborn +7117 ENCFF940DUI /home/drk/tillage/datasets/human/rna/encode/ENCSR672NDZ/summary/coverage.w5 768 384 0.3 sum_sqrt 7117 RNA:K562 treated with 10 nM Chaetocin for 12 hours +7118 ENCFF325GTZ /home/drk/tillage/datasets/human/rna/encode/ENCSR672OYP/summary/coverage.w5 768 384 0.3 sum_sqrt 7118 RNA:immature natural killer cell +7119 ENCFF248FOA /home/drk/tillage/datasets/human/rna/encode/ENCSR673DJS/summary/coverage.w5 768 384 0.3 sum_sqrt 7119 RNA:with multiple sclerosis; CD4-positive, alpha-beta memory T cell +7120 ENCFF118IXU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR673UKZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7121 RNA:WTC11 +7121 ENCFF118IXU- /home/drk/tillage/datasets/human/rna/encode/ENCSR673UKZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7120 RNA:WTC11 +7122 ENCFF985BPB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR674KHG/summary/coverage+.w5 768 384 0.3 sum_sqrt 7123 RNA:mucosa of descending colon tissue male adult (40 years) +7123 ENCFF985BPB- /home/drk/tillage/datasets/human/rna/encode/ENCSR674KHG/summary/coverage-.w5 768 384 0.3 sum_sqrt 7122 RNA:mucosa of descending colon tissue male adult (40 years) +7124 ENCFF643ZAD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR675YAS/summary/coverage+.w5 768 384 0.3 sum_sqrt 7125 RNA:right cardiac atrium tissue male adult (34 years) +7125 ENCFF643ZAD- /home/drk/tillage/datasets/human/rna/encode/ENCSR675YAS/summary/coverage-.w5 768 384 0.3 sum_sqrt 7124 RNA:right cardiac atrium tissue male adult (34 years) +7126 ENCFF565FOF /home/drk/tillage/datasets/human/rna/encode/ENCSR677MYO/summary/coverage.w5 768 384 0.3 sum_sqrt 7126 RNA:muscle of arm tissue embryo (101 days) +7127 ENCFF532MCC /home/drk/tillage/datasets/human/rna/encode/ENCSR678LBL/summary/coverage.w5 768 384 0.3 sum_sqrt 7127 RNA:IgD-negative memory B cell +7128 ENCFF340TAG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR678TMV/summary/coverage+.w5 768 384 0.3 sum_sqrt 7129 RNA:gastrocnemius medialis tissue female adult (53 years) +7129 ENCFF340TAG- /home/drk/tillage/datasets/human/rna/encode/ENCSR678TMV/summary/coverage-.w5 768 384 0.3 sum_sqrt 7128 RNA:gastrocnemius medialis tissue female adult (53 years) +7130 ENCFF064KKA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR680AAZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7131 RNA:adrenal gland tissue male adult (21 years) +7131 ENCFF064KKA- /home/drk/tillage/datasets/human/rna/encode/ENCSR680AAZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7130 RNA:adrenal gland tissue male adult (21 years) +7132 ENCFF544MJM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR680USE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7133 RNA:hair follicular keratinocyte male adult (55 years) +7133 ENCFF544MJM- /home/drk/tillage/datasets/human/rna/encode/ENCSR680USE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7132 RNA:hair follicular keratinocyte male adult (55 years) +7134 ENCFF838WFU /home/drk/tillage/datasets/human/rna/encode/ENCSR681ALA/summary/coverage.w5 768 384 0.3 sum_sqrt 7134 RNA:fibroblast of skin of abdomen male embryo (97 days) +7135 ENCFF267DQT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR686JJB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7136 RNA:adipose tissue tissue female adult (30 years) +7136 ENCFF267DQT- /home/drk/tillage/datasets/human/rna/encode/ENCSR686JJB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7135 RNA:adipose tissue tissue female adult (30 years) +7137 ENCFF166WWA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR687HJY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7138 RNA:thyroid gland tissue female adult (51 years) +7138 ENCFF166WWA- /home/drk/tillage/datasets/human/rna/encode/ENCSR687HJY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7137 RNA:thyroid gland tissue female adult (51 years) +7139 ENCFF662LZH /home/drk/tillage/datasets/human/rna/encode/ENCSR688YOZ/summary/coverage.w5 768 384 0.3 sum_sqrt 7139 RNA:adrenal gland tissue male embryo (108 days) +7140 ENCFF082CYK /home/drk/tillage/datasets/human/rna/encode/ENCSR689NPY/summary/coverage.w5 768 384 0.3 sum_sqrt 7140 RNA:K562 treated with 10 uM AR-42 for 24 hours +7141 ENCFF334KVA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR692DIM/summary/coverage+.w5 768 384 0.3 sum_sqrt 7142 RNA:naive thymus-derived CD8-positive, alpha-beta T cell male adult (30 years) +7142 ENCFF334KVA- /home/drk/tillage/datasets/human/rna/encode/ENCSR692DIM/summary/coverage-.w5 768 384 0.3 sum_sqrt 7141 RNA:naive thymus-derived CD8-positive, alpha-beta T cell male adult (30 years) +7143 ENCFF205MJV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR693CSQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7144 RNA:heart left ventricle tissue male child (3 years) +7144 ENCFF205MJV- /home/drk/tillage/datasets/human/rna/encode/ENCSR693CSQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7143 RNA:heart left ventricle tissue male child (3 years) +7145 ENCFF134ALH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR693GGB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7146 RNA:testis tissue male adult (44 years) +7146 ENCFF134ALH- /home/drk/tillage/datasets/human/rna/encode/ENCSR693GGB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7145 RNA:testis tissue male adult (44 years) +7147 ENCFF652PJM /home/drk/tillage/datasets/human/rna/encode/ENCSR693JOK/summary/coverage.w5 768 384 0.3 sum_sqrt 7147 RNA:K562 treated with 100 nM GSK J4 for 24 hours +7148 ENCFF927ANS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR693KOP/summary/coverage+.w5 768 384 0.3 sum_sqrt 7149 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (86 years) +7149 ENCFF927ANS- /home/drk/tillage/datasets/human/rna/encode/ENCSR693KOP/summary/coverage-.w5 768 384 0.3 sum_sqrt 7148 RNA:with Alzheimer's disease; middle frontal area 46 tissue female adult (86 years) +7150 ENCFF632MAZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR694AWV/summary/coverage+.w5 768 384 0.3 sum_sqrt 7151 RNA:activated CD4-positive, alpha-beta memory T cell male adult (43 years) +7151 ENCFF632MAZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR694AWV/summary/coverage-.w5 768 384 0.3 sum_sqrt 7150 RNA:activated CD4-positive, alpha-beta memory T cell male adult (43 years) +7152 ENCFF940PJY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR696SMK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7153 RNA:M059J +7153 ENCFF940PJY- /home/drk/tillage/datasets/human/rna/encode/ENCSR696SMK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7152 RNA:M059J +7154 ENCFF221JZR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR696YIB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7155 RNA:K562 insoluble cytoplasmic fraction +7155 ENCFF221JZR- /home/drk/tillage/datasets/human/rna/encode/ENCSR696YIB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7154 RNA:K562 insoluble cytoplasmic fraction +7156 ENCFF730BTN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR697EYE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7157 RNA:foreskin melanocyte male newborn +7157 ENCFF730BTN- /home/drk/tillage/datasets/human/rna/encode/ENCSR697EYE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7156 RNA:foreskin melanocyte male newborn +7158 ENCFF087ORU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR698RPL/summary/coverage+.w5 768 384 0.3 sum_sqrt 7159 RNA:HCT116 +7159 ENCFF087ORU- /home/drk/tillage/datasets/human/rna/encode/ENCSR698RPL/summary/coverage-.w5 768 384 0.3 sum_sqrt 7158 RNA:HCT116 +7160 ENCFF594TMO /home/drk/tillage/datasets/human/rna/encode/ENCSR699YJR/summary/coverage.w5 768 384 0.3 sum_sqrt 7160 RNA:muscle of leg tissue female embryo (113 days) +7161 ENCFF101ASV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR700BEW/summary/coverage+.w5 768 384 0.3 sum_sqrt 7162 RNA:mesendoderm originated from H1 +7162 ENCFF101ASV- /home/drk/tillage/datasets/human/rna/encode/ENCSR700BEW/summary/coverage-.w5 768 384 0.3 sum_sqrt 7161 RNA:mesendoderm originated from H1 +7163 ENCFF610OAY /home/drk/tillage/datasets/human/rna/encode/ENCSR700QVJ/summary/coverage.w5 768 384 0.3 sum_sqrt 7163 RNA:spleen tissue male embryo (120 days) +7164 ENCFF930CLZ /home/drk/tillage/datasets/human/rna/encode/ENCSR701JXD/summary/coverage.w5 768 384 0.3 sum_sqrt 7164 RNA:with multiple sclerosis; immature natural killer cell +7165 ENCFF854EBH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR701TST/summary/coverage+.w5 768 384 0.3 sum_sqrt 7166 RNA:prostate gland tissue male adult (54 years) +7166 ENCFF854EBH- /home/drk/tillage/datasets/human/rna/encode/ENCSR701TST/summary/coverage-.w5 768 384 0.3 sum_sqrt 7165 RNA:prostate gland tissue male adult (54 years) +7167 ENCFF633OPC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR701UNO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7168 RNA:trophoblast tissue embryo (22 weeks) +7168 ENCFF633OPC- /home/drk/tillage/datasets/human/rna/encode/ENCSR701UNO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7167 RNA:trophoblast tissue embryo (22 weeks) +7169 ENCFF759QTQ /home/drk/tillage/datasets/human/rna/encode/ENCSR702IGQ/summary/coverage.w5 768 384 0.3 sum_sqrt 7169 RNA:stomach tissue female embryo (107 days) +7170 ENCFF629GCT /home/drk/tillage/datasets/human/rna/encode/ENCSR702IMR/summary/coverage.w5 768 384 0.3 sum_sqrt 7170 RNA:left kidney tissue male embryo (96 days) +7171 ENCFF777ZZR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR706XCG/summary/coverage+.w5 768 384 0.3 sum_sqrt 7172 RNA:placental basal plate tissue male embryo (16 weeks) +7172 ENCFF777ZZR- /home/drk/tillage/datasets/human/rna/encode/ENCSR706XCG/summary/coverage-.w5 768 384 0.3 sum_sqrt 7171 RNA:placental basal plate tissue male embryo (16 weeks) +7173 ENCFF911IWQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR708VVE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7174 RNA:subcutaneous adipose tissue tissue male adult (37 years) +7174 ENCFF911IWQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR708VVE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7173 RNA:subcutaneous adipose tissue tissue male adult (37 years) +7175 ENCFF771JBV /home/drk/tillage/datasets/human/rna/encode/ENCSR711NGL/summary/coverage.w5 768 384 0.3 sum_sqrt 7175 RNA:forelimb muscle tissue female embryo (108 days) +7176 ENCFF920HIF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR712BRU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7177 RNA:H9 +7177 ENCFF920HIF- /home/drk/tillage/datasets/human/rna/encode/ENCSR712BRU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7176 RNA:H9 +7178 ENCFF811FXS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR712GOC/summary/coverage+.w5 768 384 0.3 sum_sqrt 7179 RNA:H1 +7179 ENCFF811FXS- /home/drk/tillage/datasets/human/rna/encode/ENCSR712GOC/summary/coverage-.w5 768 384 0.3 sum_sqrt 7178 RNA:H1 +7180 ENCFF970CQA /home/drk/tillage/datasets/human/rna/encode/ENCSR713DXI/summary/coverage.w5 768 384 0.3 sum_sqrt 7180 RNA:IgD-negative memory B cell +7181 ENCFF112IXW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR714KDG/summary/coverage+.w5 768 384 0.3 sum_sqrt 7182 RNA:liver tissue male child (3 years) +7182 ENCFF112IXW- /home/drk/tillage/datasets/human/rna/encode/ENCSR714KDG/summary/coverage-.w5 768 384 0.3 sum_sqrt 7181 RNA:liver tissue male child (3 years) +7183 ENCFF155PWD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR714QAF/summary/coverage+.w5 768 384 0.3 sum_sqrt 7184 RNA:mole tissue female +7184 ENCFF155PWD- /home/drk/tillage/datasets/human/rna/encode/ENCSR714QAF/summary/coverage-.w5 768 384 0.3 sum_sqrt 7183 RNA:mole tissue female +7185 ENCFF697OJB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR718CDN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7186 RNA:adipose tissue tissue male child (3 years) +7186 ENCFF697OJB- /home/drk/tillage/datasets/human/rna/encode/ENCSR718CDN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7185 RNA:adipose tissue tissue male child (3 years) +7187 ENCFF350OVE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR718RTN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7188 RNA:lower lobe of left lung tissue female adult (59 years) +7188 ENCFF350OVE- /home/drk/tillage/datasets/human/rna/encode/ENCSR718RTN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7187 RNA:lower lobe of left lung tissue female adult (59 years) +7189 ENCFF481AMD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR719HRO/summary/coverage+.w5 768 384 0.6390034863451481 sum_sqrt 7190 RNA:small intestine tissue male adult (34 years) +7190 ENCFF481AMD- /home/drk/tillage/datasets/human/rna/encode/ENCSR719HRO/summary/coverage-.w5 768 384 0.6390034863451481 sum_sqrt 7189 RNA:small intestine tissue male adult (34 years) +7191 ENCFF597SVD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR719PXC/summary/coverage+.w5 768 384 0.3 sum_sqrt 7192 RNA:ascending aorta tissue female adult (53 years) +7192 ENCFF597SVD- /home/drk/tillage/datasets/human/rna/encode/ENCSR719PXC/summary/coverage-.w5 768 384 0.3 sum_sqrt 7191 RNA:ascending aorta tissue female adult (53 years) +7193 ENCFF504JQU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR721HDG/summary/coverage+.w5 768 384 0.3 sum_sqrt 7194 RNA:stomach tissue male adult (34 years) +7194 ENCFF504JQU- /home/drk/tillage/datasets/human/rna/encode/ENCSR721HDG/summary/coverage-.w5 768 384 0.3 sum_sqrt 7193 RNA:stomach tissue male adult (34 years) +7195 ENCFF751PQP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR725TPW/summary/coverage+.w5 768 384 0.3 sum_sqrt 7196 RNA:ovary tissue female adult (30 years) +7196 ENCFF751PQP- /home/drk/tillage/datasets/human/rna/encode/ENCSR725TPW/summary/coverage-.w5 768 384 0.3 sum_sqrt 7195 RNA:ovary tissue female adult (30 years) +7197 ENCFF753LZJ /home/drk/tillage/datasets/human/rna/encode/ENCSR727VTD/summary/coverage.w5 768 384 0.3 sum_sqrt 7197 RNA:ovary tissue female embryo +7198 ENCFF900XSJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR729CAZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7199 RNA:omental fat pad tissue male adult (37 years) +7199 ENCFF900XSJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR729CAZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7198 RNA:omental fat pad tissue male adult (37 years) +7200 ENCFF590WBY /home/drk/tillage/datasets/human/rna/encode/ENCSR729ZII/summary/coverage.w5 768 384 0.3 sum_sqrt 7200 RNA:muscle of back tissue male embryo (91 days) +7201 ENCFF225CYB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR733JBX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7202 RNA:progenitor cell of endocrine pancreas +7202 ENCFF225CYB- /home/drk/tillage/datasets/human/rna/encode/ENCSR733JBX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7201 RNA:progenitor cell of endocrine pancreas +7203 ENCFF457QEG /home/drk/tillage/datasets/human/rna/encode/ENCSR733MWN/summary/coverage.w5 768 384 0.3 sum_sqrt 7203 RNA:left lung tissue male embryo (91 days) +7204 ENCFF817LFV /home/drk/tillage/datasets/human/rna/encode/ENCSR733QST/summary/coverage.w5 768 384 0.3 sum_sqrt 7204 RNA:K562 treated with 7.5 nM Panobinostat for 24 hours +7205 ENCFF381OAF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR735JKB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7206 RNA:HFFc6 +7206 ENCFF381OAF- /home/drk/tillage/datasets/human/rna/encode/ENCSR735JKB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7205 RNA:HFFc6 +7207 ENCFF629VCP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR738PHQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7208 RNA:HUES64 +7208 ENCFF629VCP- /home/drk/tillage/datasets/human/rna/encode/ENCSR738PHQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7207 RNA:HUES64 +7209 ENCFF274KQB /home/drk/tillage/datasets/human/rna/encode/ENCSR738ZHN/summary/coverage.w5 768 384 0.3 sum_sqrt 7209 RNA:K562 treated with 10 uM Crizotinib for 12 hours +7210 ENCFF558ZAJ /home/drk/tillage/datasets/human/rna/encode/ENCSR740OPV/summary/coverage.w5 768 384 0.3 sum_sqrt 7210 RNA:adrenal gland tissue female embryo (108 days) +7211 ENCFF553LFH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR740YMS/summary/coverage+.w5 768 384 0.3 sum_sqrt 7212 RNA:gastroesophageal sphincter tissue female adult (53 years) +7212 ENCFF553LFH- /home/drk/tillage/datasets/human/rna/encode/ENCSR740YMS/summary/coverage-.w5 768 384 0.3 sum_sqrt 7211 RNA:gastroesophageal sphincter tissue female adult (53 years) +7213 ENCFF056UVT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR741MLF/summary/coverage+.w5 768 384 0.3 sum_sqrt 7214 RNA:chorion tissue male embryo (16 weeks) +7214 ENCFF056UVT- /home/drk/tillage/datasets/human/rna/encode/ENCSR741MLF/summary/coverage-.w5 768 384 0.3 sum_sqrt 7213 RNA:chorion tissue male embryo (16 weeks) +7215 ENCFF206OGU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR741QEH/summary/coverage+.w5 768 384 0.3480142405063291 sum_sqrt 7216 RNA:adipose tissue tissue male adult (34 years) +7216 ENCFF206OGU- /home/drk/tillage/datasets/human/rna/encode/ENCSR741QEH/summary/coverage-.w5 768 384 0.3480142405063291 sum_sqrt 7215 RNA:adipose tissue tissue male adult (34 years) +7217 ENCFF682NDW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR743GKS/summary/coverage+.w5 768 384 0.3 sum_sqrt 7218 RNA:PC-9 +7218 ENCFF682NDW- /home/drk/tillage/datasets/human/rna/encode/ENCSR743GKS/summary/coverage-.w5 768 384 0.3 sum_sqrt 7217 RNA:PC-9 +7219 ENCFF689BPI /home/drk/tillage/datasets/human/rna/encode/ENCSR748GVH/summary/coverage.w5 768 384 0.3 sum_sqrt 7219 RNA:GM23338 originated from GM23248 +7220 ENCFF008POE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR750ETS/summary/coverage+.w5 768 384 0.3 sum_sqrt 7221 RNA:esophagus muscularis mucosa tissue male adult (54 years) +7221 ENCFF008POE- /home/drk/tillage/datasets/human/rna/encode/ENCSR750ETS/summary/coverage-.w5 768 384 0.3 sum_sqrt 7220 RNA:esophagus muscularis mucosa tissue male adult (54 years) +7222 ENCFF056FRZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR752UNJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7223 RNA:stomach tissue female adult (53 years) +7223 ENCFF056FRZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR752UNJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7222 RNA:stomach tissue female adult (53 years) +7224 ENCFF349IKE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR754WLW/summary/coverage+.w5 768 384 0.3 sum_sqrt 7225 RNA:adrenal gland tissue female adult (53 years) +7225 ENCFF349IKE- /home/drk/tillage/datasets/human/rna/encode/ENCSR754WLW/summary/coverage-.w5 768 384 0.3 sum_sqrt 7224 RNA:adrenal gland tissue female adult (53 years) +7226 ENCFF012MMA /home/drk/tillage/datasets/human/rna/encode/ENCSR755ARW/summary/coverage.w5 768 384 0.3 sum_sqrt 7226 RNA:naive thymus-derived CD4-positive, alpha-beta T cell +7227 ENCFF193HUI /home/drk/tillage/datasets/human/rna/encode/ENCSR755LFM/summary/coverage.w5 768 384 0.3 sum_sqrt 7227 RNA:testis tissue male embryo +7228 ENCFF988LZV /home/drk/tillage/datasets/human/rna/encode/ENCSR758BAT/summary/coverage.w5 768 384 0.3 sum_sqrt 7228 RNA:K562 treated with 50 uM C646 for 4 hours +7229 ENCFF541ZMB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR759TPN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7230 RNA:left colon tissue female adult (59 years) +7230 ENCFF541ZMB- /home/drk/tillage/datasets/human/rna/encode/ENCSR759TPN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7229 RNA:left colon tissue female adult (59 years) +7231 ENCFF099RCL /home/drk/tillage/datasets/human/rna/encode/ENCSR759WPF/summary/coverage.w5 768 384 0.3 sum_sqrt 7231 RNA:left renal cortex interstitium tissue male embryo (120 days) +7232 ENCFF024MEB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR761SHI/summary/coverage+.w5 768 384 0.3 sum_sqrt 7233 RNA:neural crest cell +7233 ENCFF024MEB- /home/drk/tillage/datasets/human/rna/encode/ENCSR761SHI/summary/coverage-.w5 768 384 0.3 sum_sqrt 7232 RNA:neural crest cell +7234 ENCFF498CLL /home/drk/tillage/datasets/human/rna/encode/ENCSR761ZWF/summary/coverage.w5 768 384 0.3 sum_sqrt 7234 RNA:with multiple sclerosis; CD4-positive, CD25-positive, alpha-beta regulatory T cell +7235 ENCFF382VRE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR762CJN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7236 RNA:trophoblast cell originated from H1 +7236 ENCFF382VRE- /home/drk/tillage/datasets/human/rna/encode/ENCSR762CJN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7235 RNA:trophoblast cell originated from H1 +7237 ENCFF805SZS /home/drk/tillage/datasets/human/rna/encode/ENCSR763CQW/summary/coverage.w5 768 384 0.3 sum_sqrt 7237 RNA:T-cell male adult (37 years) +7238 ENCFF386YGS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR763NOO/summary/coverage+.w5 768 384 0.4277421236872812 sum_sqrt 7239 RNA:aorta tissue male adult (34 years) +7239 ENCFF386YGS- /home/drk/tillage/datasets/human/rna/encode/ENCSR763NOO/summary/coverage-.w5 768 384 0.4277421236872812 sum_sqrt 7238 RNA:aorta tissue male adult (34 years) +7240 ENCFF133LYJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR763OMY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7241 RNA:adrenal gland tissue female adult (41 years) +7241 ENCFF133LYJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR763OMY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7240 RNA:adrenal gland tissue female adult (41 years) +7242 ENCFF343JCX /home/drk/tillage/datasets/human/rna/encode/ENCSR764EGD/summary/coverage.w5 768 384 0.3 sum_sqrt 7242 RNA:with multiple sclerosis; CD8-positive, alpha-beta memory T cell +7243 ENCFF366WMR /home/drk/tillage/datasets/human/rna/encode/ENCSR766TSI/summary/coverage.w5 768 384 0.3 sum_sqrt 7243 RNA:with multiple sclerosis; immature natural killer cell +7244 ENCFF851XAJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR769LNJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7245 RNA:heart left ventricle tissue male adult (34 years) +7245 ENCFF851XAJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR769LNJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7244 RNA:heart left ventricle tissue male adult (34 years) +7246 ENCFF270YAA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR773COB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7247 RNA:left colon tissue female adult (46 years) +7247 ENCFF270YAA- /home/drk/tillage/datasets/human/rna/encode/ENCSR773COB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7246 RNA:left colon tissue female adult (46 years) +7248 ENCFF958WEW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR774MGO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7249 RNA:chondrocyte +7249 ENCFF958WEW- /home/drk/tillage/datasets/human/rna/encode/ENCSR774MGO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7248 RNA:chondrocyte +7250 ENCFF295UWT /home/drk/tillage/datasets/human/rna/encode/ENCSR774SEX/summary/coverage.w5 768 384 0.3 sum_sqrt 7250 RNA:stomach tissue embryo (101 days) +7251 ENCFF502RUV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR775KCE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7252 RNA:thymus tissue male child (3 years) +7252 ENCFF502RUV- /home/drk/tillage/datasets/human/rna/encode/ENCSR775KCE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7251 RNA:thymus tissue male child (3 years) +7253 ENCFF259EZH /home/drk/tillage/datasets/human/rna/encode/ENCSR777ONH/summary/coverage.w5 768 384 0.3 sum_sqrt 7253 RNA:large intestine tissue male embryo (91 days) +7254 ENCFF462CKY+ /home/drk/tillage/datasets/human/rna/encode/ENCSR777TBF/summary/coverage+.w5 768 384 0.3 sum_sqrt 7255 RNA:activated CD4-positive, alpha-beta memory T cell male adult (43 years) +7255 ENCFF462CKY- /home/drk/tillage/datasets/human/rna/encode/ENCSR777TBF/summary/coverage-.w5 768 384 0.3 sum_sqrt 7254 RNA:activated CD4-positive, alpha-beta memory T cell male adult (43 years) +7256 ENCFF813JFQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR779ZJW/summary/coverage+.w5 768 384 0.3 sum_sqrt 7257 RNA:trophoblast tissue male embryo (16 weeks) +7257 ENCFF813JFQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR779ZJW/summary/coverage-.w5 768 384 0.3 sum_sqrt 7256 RNA:trophoblast tissue male embryo (16 weeks) +7258 ENCFF333ENA /home/drk/tillage/datasets/human/rna/encode/ENCSR783BUO/summary/coverage.w5 768 384 0.3 sum_sqrt 7258 RNA:stomach tissue female embryo (98 days) +7259 ENCFF924CJI /home/drk/tillage/datasets/human/rna/encode/ENCSR783SSV/summary/coverage.w5 768 384 0.3 sum_sqrt 7259 RNA:with multiple sclerosis; naive B cell +7260 ENCFF734UPN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR784PDN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7261 RNA:amnion tissue male embryo (16 weeks) +7261 ENCFF734UPN- /home/drk/tillage/datasets/human/rna/encode/ENCSR784PDN/summary/coverage-.w5 768 384 0.3 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female adult (85 years) +7268 ENCFF145JTX- /home/drk/tillage/datasets/human/rna/encode/ENCSR795GYH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7267 RNA:middle frontal area 46 tissue female adult (85 years) +7269 ENCFF532KPO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR796HLX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7270 RNA:tibial nerve tissue male adult (37 years) +7270 ENCFF532KPO- /home/drk/tillage/datasets/human/rna/encode/ENCSR796HLX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7269 RNA:tibial nerve tissue male adult (37 years) +7271 ENCFF321EHO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR797BPP/summary/coverage+.w5 768 384 0.3 sum_sqrt 7272 RNA:GM23248 +7272 ENCFF321EHO- /home/drk/tillage/datasets/human/rna/encode/ENCSR797BPP/summary/coverage-.w5 768 384 0.3 sum_sqrt 7271 RNA:GM23248 +7273 ENCFF722TDX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR797RXV/summary/coverage+.w5 768 384 0.3 sum_sqrt 7274 RNA:IMR-90 +7274 ENCFF722TDX- /home/drk/tillage/datasets/human/rna/encode/ENCSR797RXV/summary/coverage-.w5 768 384 0.3 sum_sqrt 7273 RNA:IMR-90 +7275 ENCFF542OVF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR800WIY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7276 RNA:transverse colon tissue female adult (53 years) +7276 ENCFF542OVF- /home/drk/tillage/datasets/human/rna/encode/ENCSR800WIY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7275 RNA:transverse colon tissue female adult (53 years) +7277 ENCFF718DUW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR801MKV/summary/coverage+.w5 768 384 0.3 sum_sqrt 7278 RNA:adrenal gland tissue female adult (51 years) +7278 ENCFF718DUW- /home/drk/tillage/datasets/human/rna/encode/ENCSR801MKV/summary/coverage-.w5 768 384 0.3 sum_sqrt 7277 RNA:adrenal gland tissue female adult (51 years) +7279 ENCFF980FZG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR802HPM/summary/coverage+.w5 768 384 0.3 sum_sqrt 7280 RNA:Peyer's patch tissue male adult (37 years) +7280 ENCFF980FZG- /home/drk/tillage/datasets/human/rna/encode/ENCSR802HPM/summary/coverage-.w5 768 384 0.3 sum_sqrt 7279 RNA:Peyer's patch tissue male adult (37 years) +7281 ENCFF875RMF /home/drk/tillage/datasets/human/rna/encode/ENCSR804NGX/summary/coverage.w5 768 384 0.3 sum_sqrt 7281 RNA:with multiple sclerosis; naive B cell +7282 ENCFF483IQJ /home/drk/tillage/datasets/human/rna/encode/ENCSR806ESH/summary/coverage.w5 768 384 0.3 sum_sqrt 7282 RNA:muscle of back tissue female embryo (98 days) +7283 ENCFF466NAU /home/drk/tillage/datasets/human/rna/encode/ENCSR806HCA/summary/coverage.w5 768 384 0.3 sum_sqrt 7283 RNA:K562 treated with 100 nM GSK J4 for 12 hours +7284 ENCFF347OLB /home/drk/tillage/datasets/human/rna/encode/ENCSR810ZKJ/summary/coverage.w5 768 384 0.3 sum_sqrt 7284 RNA:K562 treated with 5 uM JQ1 for 24 hours +7285 ENCFF372DGR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR812AKX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7286 RNA:sigmoid colon tissue male adult (54 years) +7286 ENCFF372DGR- /home/drk/tillage/datasets/human/rna/encode/ENCSR812AKX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7285 RNA:sigmoid colon tissue male adult (54 years) +7287 ENCFF495AAX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR813BDU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7288 RNA:HepG2 insoluble cytoplasmic fraction +7288 ENCFF495AAX- /home/drk/tillage/datasets/human/rna/encode/ENCSR813BDU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7287 RNA:HepG2 insoluble cytoplasmic fraction +7289 ENCFF458ASG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR815NTL/summary/coverage+.w5 768 384 0.3 sum_sqrt 7290 RNA:MCF 10A +7290 ENCFF458ASG- /home/drk/tillage/datasets/human/rna/encode/ENCSR815NTL/summary/coverage-.w5 768 384 0.3 sum_sqrt 7289 RNA:MCF 10A +7291 ENCFF818BRP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR815UVL/summary/coverage+.w5 768 384 0.3 sum_sqrt 7292 RNA:mammary microvascular endothelial cell female adult (26 years) +7292 ENCFF818BRP- /home/drk/tillage/datasets/human/rna/encode/ENCSR815UVL/summary/coverage-.w5 768 384 0.3 sum_sqrt 7291 RNA:mammary microvascular endothelial cell female adult (26 years) +7293 ENCFF573JBK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR816HLU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7294 RNA:left lung tissue male adult (40 years) +7294 ENCFF573JBK- /home/drk/tillage/datasets/human/rna/encode/ENCSR816HLU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7293 RNA:left lung tissue male adult (40 years) +7295 ENCFF740HBZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR816IZA/summary/coverage+.w5 768 384 0.3 sum_sqrt 7296 RNA:upper lobe of right lung tissue male adult (60 years) +7296 ENCFF740HBZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR816IZA/summary/coverage-.w5 768 384 0.3 sum_sqrt 7295 RNA:upper lobe of right lung tissue male adult (60 years) +7297 ENCFF903PTH /home/drk/tillage/datasets/human/rna/encode/ENCSR816TAY/summary/coverage.w5 768 384 0.3 sum_sqrt 7297 RNA:CD4-positive, CD25-positive, alpha-beta regulatory T cell +7298 ENCFF711RSC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR817TLH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7299 RNA:psoas muscle tissue male child (3 years) +7299 ENCFF711RSC- /home/drk/tillage/datasets/human/rna/encode/ENCSR817TLH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7298 RNA:psoas muscle tissue male child (3 years) +7300 ENCFF840DDQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR817WHQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7301 RNA:activated CD8-positive, alpha-beta memory T cell male adult (30 years) +7301 ENCFF840DDQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR817WHQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7300 RNA:activated CD8-positive, alpha-beta memory T cell male adult (30 years) +7302 ENCFF403PZE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR818DBU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7303 RNA:cardiac septum tissue female adult (41 years) +7303 ENCFF403PZE- /home/drk/tillage/datasets/human/rna/encode/ENCSR818DBU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7302 RNA:cardiac septum tissue female adult (41 years) +7304 ENCFF045JED+ /home/drk/tillage/datasets/human/rna/encode/ENCSR820IIL/summary/coverage+.w5 768 384 0.3 sum_sqrt 7305 RNA:activated naive CD8-positive, alpha-beta T cell male adult (30 years) +7305 ENCFF045JED- /home/drk/tillage/datasets/human/rna/encode/ENCSR820IIL/summary/coverage-.w5 768 384 0.3 sum_sqrt 7304 RNA:activated naive CD8-positive, alpha-beta T cell male adult (30 years) +7306 ENCFF509KPQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR820PHH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7307 RNA:GM12878 +7307 ENCFF509KPQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR820PHH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7306 RNA:GM12878 +7308 ENCFF745TWT /home/drk/tillage/datasets/human/rna/encode/ENCSR822AOE/summary/coverage.w5 768 384 0.3 sum_sqrt 7308 RNA:right renal cortex interstitium tissue male embryo (105 days) +7309 ENCFF595CZA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR822SUG/summary/coverage+.w5 768 384 0.3 sum_sqrt 7310 RNA:airway epithelial cell +7310 ENCFF595CZA- /home/drk/tillage/datasets/human/rna/encode/ENCSR822SUG/summary/coverage-.w5 768 384 0.3 sum_sqrt 7309 RNA:airway epithelial cell +7311 ENCFF929RPC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR825GWD/summary/coverage+.w5 768 384 2.003142076502732 sum_sqrt 7312 RNA:sigmoid colon tissue female adult (30 years) +7312 ENCFF929RPC- /home/drk/tillage/datasets/human/rna/encode/ENCSR825GWD/summary/coverage-.w5 768 384 2.003142076502732 sum_sqrt 7311 RNA:sigmoid colon tissue female adult (30 years) +7313 ENCFF577ZXA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR825UXP/summary/coverage+.w5 768 384 0.3 sum_sqrt 7314 RNA:lower lobe of right lung tissue male adult (60 years) +7314 ENCFF577ZXA- /home/drk/tillage/datasets/human/rna/encode/ENCSR825UXP/summary/coverage-.w5 768 384 0.3 sum_sqrt 7313 RNA:lower lobe of right lung tissue male adult (60 years) +7315 ENCFF118XUB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR827IXS/summary/coverage+.w5 768 384 0.3 sum_sqrt 7316 RNA:sigmoid colon tissue female adult (51 years) +7316 ENCFF118XUB- /home/drk/tillage/datasets/human/rna/encode/ENCSR827IXS/summary/coverage-.w5 768 384 0.3 sum_sqrt 7315 RNA:sigmoid colon tissue female adult (51 years) +7317 ENCFF589DYO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR828TEI/summary/coverage+.w5 768 384 0.3 sum_sqrt 7318 RNA:myotube originated from skeletal muscle myoblast +7318 ENCFF589DYO- /home/drk/tillage/datasets/human/rna/encode/ENCSR828TEI/summary/coverage-.w5 768 384 0.3 sum_sqrt 7317 RNA:myotube originated from skeletal muscle myoblast +7319 ENCFF333QAU /home/drk/tillage/datasets/human/rna/encode/ENCSR830HIN/summary/coverage.w5 768 384 0.3 sum_sqrt 7319 RNA:common myeloid progenitor, CD34-positive female adult (33 years) +7320 ENCFF553FQR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR837VMK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7321 RNA:heart left ventricle tissue female adult (46 years) +7321 ENCFF553FQR- /home/drk/tillage/datasets/human/rna/encode/ENCSR837VMK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7320 RNA:heart left ventricle tissue female adult (46 years) +7322 ENCFF512AIP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR837ZLY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7323 RNA:thoracic aorta tissue male adult (54 years) +7323 ENCFF512AIP- /home/drk/tillage/datasets/human/rna/encode/ENCSR837ZLY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7322 RNA:thoracic aorta tissue male adult (54 years) +7324 ENCFF668DGV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR838XNO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7325 RNA:mesenteric fat pad tissue female adult (59 years) +7325 ENCFF668DGV- /home/drk/tillage/datasets/human/rna/encode/ENCSR838XNO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7324 RNA:mesenteric fat pad tissue female adult (59 years) +7326 ENCFF237XXC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR839ZDH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7327 RNA:upper lobe of left lung tissue male adult (54 years) +7327 ENCFF237XXC- /home/drk/tillage/datasets/human/rna/encode/ENCSR839ZDH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7326 RNA:upper lobe of left lung tissue male adult (54 years) +7328 ENCFF368TTD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR841ADZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7329 RNA:ovary tissue female adult (53 years) +7329 ENCFF368TTD- /home/drk/tillage/datasets/human/rna/encode/ENCSR841ADZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7328 RNA:ovary tissue female adult (53 years) +7330 ENCFF863HRX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR841QAC/summary/coverage+.w5 768 384 0.3 sum_sqrt 7331 RNA:HFFc6 +7331 ENCFF863HRX- /home/drk/tillage/datasets/human/rna/encode/ENCSR841QAC/summary/coverage-.w5 768 384 0.3 sum_sqrt 7330 RNA:HFFc6 +7332 ENCFF999ARF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR843HXR/summary/coverage+.w5 768 384 0.3 sum_sqrt 7333 RNA:psoas muscle tissue male adult (34 years) +7333 ENCFF999ARF- /home/drk/tillage/datasets/human/rna/encode/ENCSR843HXR/summary/coverage-.w5 768 384 0.3 sum_sqrt 7332 RNA:psoas muscle tissue male adult (34 years) +7334 ENCFF463TDW /home/drk/tillage/datasets/human/rna/encode/ENCSR843RJV/summary/coverage.w5 768 384 0.3 sum_sqrt 7334 RNA:GM12878 +7335 ENCFF685VLN /home/drk/tillage/datasets/human/rna/encode/ENCSR844RSF/summary/coverage.w5 768 384 0.3 sum_sqrt 7335 RNA:K562 treated with 7.5 nM Vorinostat for 24 hours +7336 ENCFF203UBD+ /home/drk/tillage/datasets/human/rna/encode/ENCSR844SCP/summary/coverage+.w5 768 384 0.3 sum_sqrt 7337 RNA:activated T-cell male adult (38 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours +7337 ENCFF203UBD- /home/drk/tillage/datasets/human/rna/encode/ENCSR844SCP/summary/coverage-.w5 768 384 0.3 sum_sqrt 7336 RNA:activated T-cell male adult (38 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours +7338 ENCFF918AOG /home/drk/tillage/datasets/human/rna/encode/ENCSR849RVP/summary/coverage.w5 768 384 0.3 sum_sqrt 7338 RNA:with multiple sclerosis; CD8-positive, alpha-beta memory T cell +7339 ENCFF255CRM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR851BRK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7340 RNA:ectodermal cell originated from HUES64 +7340 ENCFF255CRM- /home/drk/tillage/datasets/human/rna/encode/ENCSR851BRK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7339 RNA:ectodermal cell originated from HUES64 +7341 ENCFF734OLC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR851GNB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7342 RNA:foreskin fibroblast male newborn +7342 ENCFF734OLC- /home/drk/tillage/datasets/human/rna/encode/ENCSR851GNB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7341 RNA:foreskin fibroblast male newborn +7343 ENCFF563AJC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR853BNH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7344 RNA:gastrocnemius medialis tissue male adult (37 years) +7344 ENCFF563AJC- /home/drk/tillage/datasets/human/rna/encode/ENCSR853BNH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7343 RNA:gastrocnemius medialis tissue male adult (37 years) +7345 ENCFF756IDW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR853TXT/summary/coverage+.w5 768 384 0.3 sum_sqrt 7346 RNA:right cardiac atrium tissue male adult (60 years) +7346 ENCFF756IDW- /home/drk/tillage/datasets/human/rna/encode/ENCSR853TXT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7345 RNA:right cardiac atrium tissue male adult (60 years) +7347 ENCFF818TKM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR853WOM/summary/coverage+.w5 768 384 0.3 sum_sqrt 7348 RNA:stomach tissue female adult (51 years) +7348 ENCFF818TKM- /home/drk/tillage/datasets/human/rna/encode/ENCSR853WOM/summary/coverage-.w5 768 384 0.3 sum_sqrt 7347 RNA:stomach tissue female adult (51 years) +7349 ENCFF918QTH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR856VAD/summary/coverage+.w5 768 384 0.3 sum_sqrt 7350 RNA:activated CD4-positive, alpha-beta memory T cell male adult (43 years) +7350 ENCFF918QTH- /home/drk/tillage/datasets/human/rna/encode/ENCSR856VAD/summary/coverage-.w5 768 384 0.3 sum_sqrt 7349 RNA:activated CD4-positive, alpha-beta memory T cell male adult (43 years) +7351 ENCFF444MUM /home/drk/tillage/datasets/human/rna/encode/ENCSR857VKL/summary/coverage.w5 768 384 0.3 sum_sqrt 7351 RNA:large intestine tissue female embryo (98 days) +7352 ENCFF593EJA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR857WJK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7353 RNA:sigmoid colon tissue male adult (37 years) +7353 ENCFF593EJA- /home/drk/tillage/datasets/human/rna/encode/ENCSR857WJK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7352 RNA:sigmoid colon tissue male adult (37 years) +7354 ENCFF108RDF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR858QEL/summary/coverage+.w5 768 384 0.3 sum_sqrt 7355 RNA:tibial nerve tissue female adult (53 years) +7355 ENCFF108RDF- /home/drk/tillage/datasets/human/rna/encode/ENCSR858QEL/summary/coverage-.w5 768 384 0.3 sum_sqrt 7354 RNA:tibial nerve tissue female adult (53 years) +7356 ENCFF238NVT /home/drk/tillage/datasets/human/rna/encode/ENCSR859HWB/summary/coverage.w5 768 384 0.3 sum_sqrt 7356 RNA:hepatocyte originated from H9 +7357 ENCFF946QQD /home/drk/tillage/datasets/human/rna/encode/ENCSR859KGW/summary/coverage.w5 768 384 0.3 sum_sqrt 7357 RNA:large intestine tissue female embryo (85 days) +7358 ENCFF490SYS /home/drk/tillage/datasets/human/rna/encode/ENCSR860DST/summary/coverage.w5 768 384 0.3 sum_sqrt 7358 RNA:muscle of leg tissue male embryo (96 days) +7359 ENCFF837YDW+ /home/drk/tillage/datasets/human/rna/encode/ENCSR860DWK/summary/coverage+.w5 768 384 0.3 sum_sqrt 7360 RNA:K562 cytosolic fraction +7360 ENCFF837YDW- /home/drk/tillage/datasets/human/rna/encode/ENCSR860DWK/summary/coverage-.w5 768 384 0.3 sum_sqrt 7359 RNA:K562 cytosolic fraction +7361 ENCFF300QBN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR860HAA/summary/coverage+.w5 768 384 0.3 sum_sqrt 7362 RNA:mammary epithelial cell female adult (17 years) +7362 ENCFF300QBN- /home/drk/tillage/datasets/human/rna/encode/ENCSR860HAA/summary/coverage-.w5 768 384 0.3 sum_sqrt 7361 RNA:mammary epithelial cell female adult (17 years) +7363 ENCFF104DTS /home/drk/tillage/datasets/human/rna/encode/ENCSR861QKF/summary/coverage.w5 768 384 0.3 sum_sqrt 7363 RNA:CD8-positive, alpha-beta T cell male adult (37 years) +7364 ENCFF551UCO /home/drk/tillage/datasets/human/rna/encode/ENCSR861SOG/summary/coverage.w5 768 384 0.3 sum_sqrt 7364 RNA:left lung tissue female embryo (108 days) +7365 ENCFF853VJV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR862HPO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7366 RNA:HepG2 cytosolic fraction +7366 ENCFF853VJV- /home/drk/tillage/datasets/human/rna/encode/ENCSR862HPO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7365 RNA:HepG2 cytosolic fraction +7367 ENCFF726WTR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR862RGX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7368 RNA:suprapubic skin tissue male adult (37 years) +7368 ENCFF726WTR- /home/drk/tillage/datasets/human/rna/encode/ENCSR862RGX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7367 RNA:suprapubic skin tissue male adult (37 years) +7369 ENCFF458XQS /home/drk/tillage/datasets/human/rna/encode/ENCSR863BUL/summary/coverage.w5 768 384 0.3 sum_sqrt 7369 RNA:heart tissue female embryo (91 days) +7370 ENCFF193HXZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR863VFU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7371 RNA:middle frontal area 46 tissue female adult (88 years) +7371 ENCFF193HXZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR863VFU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7370 RNA:middle frontal area 46 tissue female adult (88 years) +7372 ENCFF289VET /home/drk/tillage/datasets/human/rna/encode/ENCSR866UOA/summary/coverage.w5 768 384 0.3 sum_sqrt 7372 RNA:K562 treated with 7.5 nM Panobinostat for 4 hours +7373 ENCFF858QRQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR867WQC/summary/coverage+.w5 768 384 0.3 sum_sqrt 7374 RNA:right cardiac atrium tissue male adult (40 years) +7374 ENCFF858QRQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR867WQC/summary/coverage-.w5 768 384 0.3 sum_sqrt 7373 RNA:right cardiac atrium tissue male adult (40 years) +7375 ENCFF096CZT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR872LTT/summary/coverage+.w5 768 384 0.3 sum_sqrt 7376 RNA:ectodermal cell originated from HUES64 +7376 ENCFF096CZT- /home/drk/tillage/datasets/human/rna/encode/ENCSR872LTT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7375 RNA:ectodermal cell originated from HUES64 +7377 ENCFF701JUX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR875MVZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7378 RNA:with Alzheimer's disease; middle frontal area 46 tissue male adult (90 or above years) +7378 ENCFF701JUX- /home/drk/tillage/datasets/human/rna/encode/ENCSR875MVZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7377 RNA:with Alzheimer's disease; middle frontal area 46 tissue male adult (90 or above years) +7379 ENCFF571AFR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR876TAN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7380 RNA:left ventricle myocardium superior tissue male adult (60 years) +7380 ENCFF571AFR- /home/drk/tillage/datasets/human/rna/encode/ENCSR876TAN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7379 RNA:left ventricle myocardium superior tissue male adult (60 years) +7381 ENCFF163AGZ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR877FRY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7382 RNA:excitatory neuron +7382 ENCFF163AGZ- /home/drk/tillage/datasets/human/rna/encode/ENCSR877FRY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7381 RNA:excitatory neuron +7383 ENCFF863JIL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR878EUT/summary/coverage+.w5 768 384 0.3 sum_sqrt 7384 RNA:glomerular endothelial cell female embryo (22 weeks) and male embryo (22 weeks) +7384 ENCFF863JIL- /home/drk/tillage/datasets/human/rna/encode/ENCSR878EUT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7383 RNA:glomerular endothelial cell female embryo (22 weeks) and male embryo (22 weeks) +7385 ENCFF318MTJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR880EGO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7386 RNA:SJSA1 +7386 ENCFF318MTJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR880EGO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7385 RNA:SJSA1 +7387 ENCFF107LVE /home/drk/tillage/datasets/human/rna/encode/ENCSR880XLM/summary/coverage.w5 768 384 0.3 sum_sqrt 7387 RNA:placenta tissue female embryo (113 days) +7388 ENCFF432UNL /home/drk/tillage/datasets/human/rna/encode/ENCSR882NWV/summary/coverage.w5 768 384 0.3 sum_sqrt 7388 RNA:K562 treated with 50 uM C646 for 24 hours +7389 ENCFF717QBH /home/drk/tillage/datasets/human/rna/encode/ENCSR884EVS/summary/coverage.w5 768 384 0.3 sum_sqrt 7389 RNA:right renal cortex interstitium tissue male embryo (120 days) +7390 ENCFF278EZT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR885DVH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7391 RNA:K562 +7391 ENCFF278EZT- /home/drk/tillage/datasets/human/rna/encode/ENCSR885DVH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7390 RNA:K562 +7392 ENCFF990JTR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR887ZSY/summary/coverage+.w5 768 384 0.3 sum_sqrt 7393 RNA:HepG2 membrane fraction +7393 ENCFF990JTR- /home/drk/tillage/datasets/human/rna/encode/ENCSR887ZSY/summary/coverage-.w5 768 384 0.3 sum_sqrt 7392 RNA:HepG2 membrane fraction +7394 ENCFF279MVV /home/drk/tillage/datasets/human/rna/encode/ENCSR889TRN/summary/coverage.w5 768 384 0.3 sum_sqrt 7394 RNA:GM12878 +7395 ENCFF343WYY /home/drk/tillage/datasets/human/rna/encode/ENCSR891JVD/summary/coverage.w5 768 384 0.3 sum_sqrt 7395 RNA:muscle of back tissue male embryo (127 days) +7396 ENCFF649RYB+ /home/drk/tillage/datasets/human/rna/encode/ENCSR892LBU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7397 RNA:kidney tissue female adult (47 years) +7397 ENCFF649RYB- /home/drk/tillage/datasets/human/rna/encode/ENCSR892LBU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7396 RNA:kidney tissue female adult (47 years) +7398 ENCFF982WYX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR894WMQ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7399 RNA:myocyte originated from LHCN-M2 +7399 ENCFF982WYX- /home/drk/tillage/datasets/human/rna/encode/ENCSR894WMQ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7398 RNA:myocyte originated from LHCN-M2 +7400 ENCFF031QGE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR895ZTB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7401 RNA:H1 +7401 ENCFF031QGE- /home/drk/tillage/datasets/human/rna/encode/ENCSR895ZTB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7400 RNA:H1 +7402 ENCFF168RPD /home/drk/tillage/datasets/human/rna/encode/ENCSR896QPD/summary/coverage.w5 768 384 0.3 sum_sqrt 7402 RNA:kidney tissue female embryo (85 days) +7403 ENCFF873UUS+ /home/drk/tillage/datasets/human/rna/encode/ENCSR897JEH/summary/coverage+.w5 768 384 0.3 sum_sqrt 7404 RNA:Calu3 +7404 ENCFF873UUS- /home/drk/tillage/datasets/human/rna/encode/ENCSR897JEH/summary/coverage-.w5 768 384 0.3 sum_sqrt 7403 RNA:Calu3 +7405 ENCFF734VZN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR897KTO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7406 RNA:epithelial cell of alveolus of lung NONE and female embryo (21 weeks) +7406 ENCFF734VZN- /home/drk/tillage/datasets/human/rna/encode/ENCSR897KTO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7405 RNA:epithelial cell of alveolus of lung NONE and female embryo (21 weeks) +7407 ENCFF801IUE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR899IVV/summary/coverage+.w5 768 384 0.3 sum_sqrt 7408 RNA:stimulated activated CD4-positive, alpha-beta T cell male adult (20 years) treated with 10 ng/mL Interleukin-2, anti-CD3 and anti-CD28 coated beads +7408 ENCFF801IUE- /home/drk/tillage/datasets/human/rna/encode/ENCSR899IVV/summary/coverage-.w5 768 384 0.3 sum_sqrt 7407 RNA:stimulated activated CD4-positive, alpha-beta T cell male adult (20 years) treated with 10 ng/mL Interleukin-2, anti-CD3 and anti-CD28 coated beads +7409 ENCFF473FLK /home/drk/tillage/datasets/human/rna/encode/ENCSR899NLW/summary/coverage.w5 768 384 0.3 sum_sqrt 7409 RNA:spinal cord tissue male embryo (96 days) +7410 ENCFF297UUV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR899OKE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7411 RNA:placenta tissue female embryo +7411 ENCFF297UUV- /home/drk/tillage/datasets/human/rna/encode/ENCSR899OKE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7410 RNA:placenta tissue female embryo +7412 ENCFF860TYK /home/drk/tillage/datasets/human/rna/encode/ENCSR899SWV/summary/coverage.w5 768 384 0.3 sum_sqrt 7412 RNA:renal cortex interstitium tissue female embryo (120 days) +7413 ENCFF544TFG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR900DUO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7414 RNA:activated T-cell female adult (33 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours +7414 ENCFF544TFG- /home/drk/tillage/datasets/human/rna/encode/ENCSR900DUO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7413 RNA:activated T-cell female adult (33 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours +7415 ENCFF353PFR+ /home/drk/tillage/datasets/human/rna/encode/ENCSR900FUP/summary/coverage+.w5 768 384 0.3 sum_sqrt 7416 RNA:heart left ventricle tissue female adult (59 years) +7416 ENCFF353PFR- /home/drk/tillage/datasets/human/rna/encode/ENCSR900FUP/summary/coverage-.w5 768 384 0.3 sum_sqrt 7415 RNA:heart left ventricle tissue female adult (59 years) +7417 ENCFF496TSR /home/drk/tillage/datasets/human/rna/encode/ENCSR900IJI/summary/coverage.w5 768 384 0.3 sum_sqrt 7417 RNA:K562 treated with 10 nM Bortezomib for 24 hours +7418 ENCFF726SGF /home/drk/tillage/datasets/human/rna/encode/ENCSR900JSG/summary/coverage.w5 768 384 0.3 sum_sqrt 7418 RNA:Purkinje cell male child (6 years) +7419 ENCFF359MDK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR900SGE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7420 RNA:spleen tissue female adult (53 years) +7420 ENCFF359MDK- /home/drk/tillage/datasets/human/rna/encode/ENCSR900SGE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7419 RNA:spleen tissue female adult (53 years) +7421 ENCFF430NYX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR903XMI/summary/coverage+.w5 768 384 0.3 sum_sqrt 7422 RNA:placenta tissue female embryo +7422 ENCFF430NYX- /home/drk/tillage/datasets/human/rna/encode/ENCSR903XMI/summary/coverage-.w5 768 384 0.3 sum_sqrt 7421 RNA:placenta tissue female embryo +7423 ENCFF926QTW /home/drk/tillage/datasets/human/rna/encode/ENCSR905LVO/summary/coverage.w5 768 384 0.3 sum_sqrt 7423 RNA:CD14-positive monocyte male adult (37 years) +7424 ENCFF318UAJ /home/drk/tillage/datasets/human/rna/encode/ENCSR906HEV/summary/coverage.w5 768 384 0.3 sum_sqrt 7424 RNA:muscle of trunk tissue female embryo (113 days) +7425 ENCFF880GSS /home/drk/tillage/datasets/human/rna/encode/ENCSR907KDH/summary/coverage.w5 768 384 0.3 sum_sqrt 7425 RNA:kidney tissue male embryo (87 days) +7426 ENCFF358IQV+ /home/drk/tillage/datasets/human/rna/encode/ENCSR908ZAS/summary/coverage+.w5 768 384 0.3 sum_sqrt 7427 RNA:hepatocyte originated from H9 +7427 ENCFF358IQV- /home/drk/tillage/datasets/human/rna/encode/ENCSR908ZAS/summary/coverage-.w5 768 384 0.3 sum_sqrt 7426 RNA:hepatocyte originated from H9 +7428 ENCFF426XDX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR910QOX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7429 RNA:spleen tissue male adult (34 years) +7429 ENCFF426XDX- /home/drk/tillage/datasets/human/rna/encode/ENCSR910QOX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7428 RNA:spleen tissue male adult (34 years) +7430 ENCFF107LSA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR911XSA/summary/coverage+.w5 768 384 0.3 sum_sqrt 7431 RNA:naive thymus-derived CD4-positive, alpha-beta T cell male adult (43 years) +7431 ENCFF107LSA- /home/drk/tillage/datasets/human/rna/encode/ENCSR911XSA/summary/coverage-.w5 768 384 0.3 sum_sqrt 7430 RNA:naive thymus-derived CD4-positive, alpha-beta T cell male adult (43 years) +7432 ENCFF043VUO+ /home/drk/tillage/datasets/human/rna/encode/ENCSR915EBZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7433 RNA:heart right ventricle tissue male adult (40 years) +7433 ENCFF043VUO- /home/drk/tillage/datasets/human/rna/encode/ENCSR915EBZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7432 RNA:heart right ventricle tissue male adult (40 years) +7434 ENCFF124RPC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR917YHC/summary/coverage+.w5 768 384 0.3 sum_sqrt 7435 RNA:lung tissue female adult (30 years) +7435 ENCFF124RPC- /home/drk/tillage/datasets/human/rna/encode/ENCSR917YHC/summary/coverage-.w5 768 384 0.3 sum_sqrt 7434 RNA:lung tissue female adult (30 years) +7436 ENCFF403HKJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR919MZM/summary/coverage+.w5 768 384 0.3 sum_sqrt 7437 RNA:endometrial microvascular endothelial cells female adult (34 years) +7437 ENCFF403HKJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR919MZM/summary/coverage-.w5 768 384 0.3 sum_sqrt 7436 RNA:endometrial microvascular endothelial cells female adult (34 years) +7438 ENCFF965MBA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR919QJT/summary/coverage+.w5 768 384 0.3 sum_sqrt 7439 RNA:H4 +7439 ENCFF965MBA- /home/drk/tillage/datasets/human/rna/encode/ENCSR919QJT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7438 RNA:H4 +7440 ENCFF123BBC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR920UAO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7441 RNA:astrocyte +7441 ENCFF123BBC- /home/drk/tillage/datasets/human/rna/encode/ENCSR920UAO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7440 RNA:astrocyte +7442 ENCFF891ALA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR922VBO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7443 RNA:stomach tissue male child (3 years) +7443 ENCFF891ALA- /home/drk/tillage/datasets/human/rna/encode/ENCSR922VBO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7442 RNA:stomach tissue male child (3 years) +7444 ENCFF974VUT+ /home/drk/tillage/datasets/human/rna/encode/ENCSR924MSZ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7445 RNA:heart left ventricle tissue male adult (40 years) +7445 ENCFF974VUT- /home/drk/tillage/datasets/human/rna/encode/ENCSR924MSZ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7444 RNA:heart left ventricle tissue male adult (40 years) +7446 ENCFF150XAC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR925GFP/summary/coverage+.w5 768 384 0.3 sum_sqrt 7447 RNA:activated CD4-positive, alpha-beta T cell male adult (20 years) treated with anti-CD3 and anti-CD28 coated beads +7447 ENCFF150XAC- /home/drk/tillage/datasets/human/rna/encode/ENCSR925GFP/summary/coverage-.w5 768 384 0.3 sum_sqrt 7446 RNA:activated CD4-positive, alpha-beta T cell male adult (20 years) treated with anti-CD3 and anti-CD28 coated beads +7448 ENCFF046NXJ /home/drk/tillage/datasets/human/rna/encode/ENCSR928CEQ/summary/coverage.w5 768 384 0.3 sum_sqrt 7448 RNA:right renal pelvis tissue male embryo (105 days) +7449 ENCFF688MII /home/drk/tillage/datasets/human/rna/encode/ENCSR929KRW/summary/coverage.w5 768 384 0.3 sum_sqrt 7449 RNA:renal pelvis tissue male embryo (97 days) +7450 ENCFF604EYK /home/drk/tillage/datasets/human/rna/encode/ENCSR930URM/summary/coverage.w5 768 384 0.3 sum_sqrt 7450 RNA:large intestine tissue female embryo (120 days) +7451 ENCFF831HGM+ /home/drk/tillage/datasets/human/rna/encode/ENCSR931WGT/summary/coverage+.w5 768 384 0.3 sum_sqrt 7452 RNA:HepG2 cytosolic fraction +7452 ENCFF831HGM- /home/drk/tillage/datasets/human/rna/encode/ENCSR931WGT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7451 RNA:HepG2 cytosolic fraction +7453 ENCFF484JKA /home/drk/tillage/datasets/human/rna/encode/ENCSR936COT/summary/coverage.w5 768 384 0.3 sum_sqrt 7453 RNA:naive B cell +7454 ENCFF850SIL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR938LSP/summary/coverage+.w5 768 384 0.3 sum_sqrt 7455 RNA:GM23338 originated from GM23248 +7455 ENCFF850SIL- /home/drk/tillage/datasets/human/rna/encode/ENCSR938LSP/summary/coverage-.w5 768 384 0.3 sum_sqrt 7454 RNA:GM23338 originated from GM23248 +7456 ENCFF956EIE /home/drk/tillage/datasets/human/rna/encode/ENCSR940EVD/summary/coverage.w5 768 384 0.3 sum_sqrt 7456 RNA:with multiple sclerosis; CD4-positive, CD25-positive, alpha-beta regulatory T cell +7457 ENCFF413WXI+ /home/drk/tillage/datasets/human/rna/encode/ENCSR942YMN/summary/coverage+.w5 768 384 0.3 sum_sqrt 7458 RNA:placenta tissue male embryo +7458 ENCFF413WXI- /home/drk/tillage/datasets/human/rna/encode/ENCSR942YMN/summary/coverage-.w5 768 384 0.3 sum_sqrt 7457 RNA:placenta tissue male embryo +7459 ENCFF315ODV /home/drk/tillage/datasets/human/rna/encode/ENCSR944FLL/summary/coverage.w5 768 384 0.3 sum_sqrt 7459 RNA:CD8-positive, alpha-beta T cell male adult (21 years) +7460 ENCFF526ILL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR944OIX/summary/coverage+.w5 768 384 0.3 sum_sqrt 7461 RNA:activated naive CD4-positive, alpha-beta T cell male adult (43 years) +7461 ENCFF526ILL- /home/drk/tillage/datasets/human/rna/encode/ENCSR944OIX/summary/coverage-.w5 768 384 0.3 sum_sqrt 7460 RNA:activated naive CD4-positive, alpha-beta T cell male adult (43 years) +7462 ENCFF346AHI /home/drk/tillage/datasets/human/rna/encode/ENCSR949BBZ/summary/coverage.w5 768 384 0.3 sum_sqrt 7462 RNA:K562 treated with 25 uM Galeterone for 12 hours +7463 ENCFF568QQJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR949UTT/summary/coverage+.w5 768 384 0.3 sum_sqrt 7464 RNA:with mild cognitive impairment; middle frontal area 46 tissue female adult (83 years) +7464 ENCFF568QQJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR949UTT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7463 RNA:with mild cognitive impairment; middle frontal area 46 tissue female adult (83 years) +7465 ENCFF333PSK /home/drk/tillage/datasets/human/rna/encode/ENCSR950YTM/summary/coverage.w5 768 384 0.3 sum_sqrt 7465 RNA:K562 treated with 7.5 nM Vorinostat for 48 hours +7466 ENCFF480XQC /home/drk/tillage/datasets/human/rna/encode/ENCSR951NPS/summary/coverage.w5 768 384 0.3 sum_sqrt 7466 RNA:stomach tissue female embryo (105 days) +7467 ENCFF496YJK+ /home/drk/tillage/datasets/human/rna/encode/ENCSR954PZB/summary/coverage+.w5 768 384 0.3 sum_sqrt 7468 RNA:adrenal gland tissue male adult (54 years) +7468 ENCFF496YJK- /home/drk/tillage/datasets/human/rna/encode/ENCSR954PZB/summary/coverage-.w5 768 384 0.3 sum_sqrt 7467 RNA:adrenal gland tissue male adult (54 years) +7469 ENCFF095UOA+ /home/drk/tillage/datasets/human/rna/encode/ENCSR956ZVR/summary/coverage+.w5 768 384 0.3 sum_sqrt 7470 RNA:naive thymus-derived CD4-positive, alpha-beta T cell male adult (43 years) +7470 ENCFF095UOA- /home/drk/tillage/datasets/human/rna/encode/ENCSR956ZVR/summary/coverage-.w5 768 384 0.3 sum_sqrt 7469 RNA:naive thymus-derived CD4-positive, alpha-beta T cell male adult (43 years) +7471 ENCFF366NWQ /home/drk/tillage/datasets/human/rna/encode/ENCSR957GVE/summary/coverage.w5 768 384 0.3 sum_sqrt 7471 RNA:K562 treated with 7.5 nM Panobinostat for 12 hours +7472 ENCFF995SOX+ /home/drk/tillage/datasets/human/rna/encode/ENCSR957WSE/summary/coverage+.w5 768 384 0.3 sum_sqrt 7473 RNA:activated naive CD8-positive, alpha-beta T cell male adult (30 years) +7473 ENCFF995SOX- /home/drk/tillage/datasets/human/rna/encode/ENCSR957WSE/summary/coverage-.w5 768 384 0.3 sum_sqrt 7472 RNA:activated naive CD8-positive, alpha-beta T cell male adult (30 years) +7474 ENCFF238RLU /home/drk/tillage/datasets/human/rna/encode/ENCSR962TBJ/summary/coverage.w5 768 384 0.3 sum_sqrt 7474 RNA:H1 +7475 ENCFF882KEH /home/drk/tillage/datasets/human/rna/encode/ENCSR963EVZ/summary/coverage.w5 768 384 0.3 sum_sqrt 7475 RNA:immature natural killer cell +7476 ENCFF314QAJ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR967BBU/summary/coverage+.w5 768 384 0.3 sum_sqrt 7477 RNA:chorionic villus tissue embryo (16 weeks) +7477 ENCFF314QAJ- /home/drk/tillage/datasets/human/rna/encode/ENCSR967BBU/summary/coverage-.w5 768 384 0.3 sum_sqrt 7476 RNA:chorionic villus tissue embryo (16 weeks) +7478 ENCFF497QCQ+ /home/drk/tillage/datasets/human/rna/encode/ENCSR967JPI/summary/coverage+.w5 768 384 0.3 sum_sqrt 7479 RNA:gastrocnemius medialis tissue male adult (54 years) +7479 ENCFF497QCQ- /home/drk/tillage/datasets/human/rna/encode/ENCSR967JPI/summary/coverage-.w5 768 384 0.3 sum_sqrt 7478 RNA:gastrocnemius medialis tissue male adult (54 years) +7480 ENCFF623LHV /home/drk/tillage/datasets/human/rna/encode/ENCSR968ACN/summary/coverage.w5 768 384 0.3 sum_sqrt 7480 RNA:with multiple sclerosis; CD14-positive monocyte +7481 ENCFF825QDH+ /home/drk/tillage/datasets/human/rna/encode/ENCSR968WKR/summary/coverage+.w5 768 384 0.3 sum_sqrt 7482 RNA:bipolar neuron originated from GM23338 treated with 0.5 ug/mL doxycycline hyclate for 4 days +7482 ENCFF825QDH- /home/drk/tillage/datasets/human/rna/encode/ENCSR968WKR/summary/coverage-.w5 768 384 0.3 sum_sqrt 7481 RNA:bipolar neuron originated from GM23338 treated with 0.5 ug/mL doxycycline hyclate for 4 days +7483 ENCFF874FQG /home/drk/tillage/datasets/human/rna/encode/ENCSR969XWI/summary/coverage.w5 768 384 0.3 sum_sqrt 7483 RNA:with multiple sclerosis; CD4-positive, alpha-beta memory T cell +7484 ENCFF045DIU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR971GPJ/summary/coverage+.w5 768 384 0.3 sum_sqrt 7485 RNA:HT-29 +7485 ENCFF045DIU- /home/drk/tillage/datasets/human/rna/encode/ENCSR971GPJ/summary/coverage-.w5 768 384 0.3 sum_sqrt 7484 RNA:HT-29 +7486 ENCFF974CXF+ /home/drk/tillage/datasets/human/rna/encode/ENCSR971KNW/summary/coverage+.w5 768 384 0.3 sum_sqrt 7487 RNA:MG63 +7487 ENCFF974CXF- /home/drk/tillage/datasets/human/rna/encode/ENCSR971KNW/summary/coverage-.w5 768 384 0.3 sum_sqrt 7486 RNA:MG63 +7488 ENCFF937GHU /home/drk/tillage/datasets/human/rna/encode/ENCSR972TMF/summary/coverage.w5 768 384 0.3 sum_sqrt 7488 RNA:immature natural killer cell +7489 ENCFF050OBT /home/drk/tillage/datasets/human/rna/encode/ENCSR975CMV/summary/coverage.w5 768 384 0.3 sum_sqrt 7489 RNA:with multiple sclerosis; IgD-negative memory B cell +7490 ENCFF373WQE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR976JGI/summary/coverage+.w5 768 384 0.3 sum_sqrt 7491 RNA:mesendoderm originated from H1 +7491 ENCFF373WQE- /home/drk/tillage/datasets/human/rna/encode/ENCSR976JGI/summary/coverage-.w5 768 384 0.3 sum_sqrt 7490 RNA:mesendoderm 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7498 RNA:HepG2 +7498 ENCFF696GRP- /home/drk/tillage/datasets/human/rna/encode/ENCSR985KAT/summary/coverage-.w5 768 384 0.3 sum_sqrt 7497 RNA:HepG2 +7499 ENCFF684CHN+ /home/drk/tillage/datasets/human/rna/encode/ENCSR989IFF/summary/coverage+.w5 768 384 0.3 sum_sqrt 7500 RNA:CD8-positive, alpha-beta memory T cell male adult (30 years) +7500 ENCFF684CHN- /home/drk/tillage/datasets/human/rna/encode/ENCSR989IFF/summary/coverage-.w5 768 384 0.3 sum_sqrt 7499 RNA:CD8-positive, alpha-beta memory T cell male adult (30 years) +7501 ENCFF304RDA /home/drk/tillage/datasets/human/rna/encode/ENCSR990LHE/summary/coverage.w5 768 384 0.3 sum_sqrt 7501 RNA:muscle of arm tissue male embryo (96 days) +7502 ENCFF057TXE+ /home/drk/tillage/datasets/human/rna/encode/ENCSR991HIR/summary/coverage+.w5 768 384 0.3 sum_sqrt 7503 RNA:lower leg skin tissue female adult (53 years) +7503 ENCFF057TXE- /home/drk/tillage/datasets/human/rna/encode/ENCSR991HIR/summary/coverage-.w5 768 384 0.3 sum_sqrt 7502 RNA:lower leg skin tissue female adult (53 years) +7504 ENCFF004DOF /home/drk/tillage/datasets/human/rna/encode/ENCSR992MUF/summary/coverage.w5 768 384 0.3 sum_sqrt 7504 RNA:CD14-positive monocyte +7505 ENCFF573WTP+ /home/drk/tillage/datasets/human/rna/encode/ENCSR993IPO/summary/coverage+.w5 768 384 0.3 sum_sqrt 7506 RNA:left cardiac atrium tissue male adult (60 years) +7506 ENCFF573WTP- /home/drk/tillage/datasets/human/rna/encode/ENCSR993IPO/summary/coverage-.w5 768 384 0.3 sum_sqrt 7505 RNA:left cardiac atrium tissue male adult (60 years) +7507 ENCFF118SVL+ /home/drk/tillage/datasets/human/rna/encode/ENCSR993JMV/summary/coverage+.w5 768 384 0.3 sum_sqrt 7508 RNA:endothelial cell of umbilical vein newborn +7508 ENCFF118SVL- /home/drk/tillage/datasets/human/rna/encode/ENCSR993JMV/summary/coverage-.w5 768 384 0.3 sum_sqrt 7507 RNA:endothelial cell of umbilical vein newborn +7509 ENCFF915WBG+ /home/drk/tillage/datasets/human/rna/encode/ENCSR993QGR/summary/coverage+.w5 768 384 0.3 sum_sqrt 7510 RNA:esophagus tissue female adult (30 years) +7510 ENCFF915WBG- /home/drk/tillage/datasets/human/rna/encode/ENCSR993QGR/summary/coverage-.w5 768 384 0.3 sum_sqrt 7509 RNA:esophagus tissue female adult (30 years) +7511 ENCFF137BCU+ /home/drk/tillage/datasets/human/rna/encode/ENCSR995BHD/summary/coverage+.w5 768 384 0.3 sum_sqrt 7512 RNA:aorta tissue female adult (30 years) +7512 ENCFF137BCU- /home/drk/tillage/datasets/human/rna/encode/ENCSR995BHD/summary/coverage-.w5 768 384 0.3 sum_sqrt 7511 RNA:aorta tissue female adult (30 years) +7513 ENCFF630CTN /home/drk/tillage/datasets/human/rna/encode/ENCSR995ORR/summary/coverage.w5 768 384 0.3 sum_sqrt 7513 RNA:muscle of back tissue female embryo (105 days) +7514 ENCFF098OUC+ /home/drk/tillage/datasets/human/rna/encode/ENCSR996OED/summary/coverage+.w5 768 384 0.3 sum_sqrt 7515 RNA:activated naive CD4-positive, alpha-beta T cell male adult (43 years) +7515 ENCFF098OUC- /home/drk/tillage/datasets/human/rna/encode/ENCSR996OED/summary/coverage-.w5 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years) +7521 ENCFF304GQR- /home/drk/tillage/datasets/human/rna/encode/ENCSR999ZCI/summary/coverage-.w5 768 384 0.7307142857142858 sum_sqrt 7520 RNA:sigmoid colon tissue male adult (34 years) +7522 GTEX-132QS-2526-SM-62LFJ.1 /home/drk/tillage/datasets/human/rna/recount3/adipose_tissue/GTEX-132QS-2526-SM-62LFJ.1/coverage.w5 768 384 0.01 sum_sqrt 7522 RNA:adipose_tissue +7523 GTEX-1GMR3-0826-SM-9WYT4.1 /home/drk/tillage/datasets/human/rna/recount3/adipose_tissue/GTEX-1GMR3-0826-SM-9WYT4.1/coverage.w5 768 384 0.01 sum_sqrt 7523 RNA:adipose_tissue +7524 GTEX-1HSEH-0226-SM-ACKVV.1 /home/drk/tillage/datasets/human/rna/recount3/adipose_tissue/GTEX-1HSEH-0226-SM-ACKVV.1/coverage.w5 768 384 0.01 sum_sqrt 7524 RNA:adipose_tissue +7525 GTEX-11GSP-0326-SM-5A5KW.1 /home/drk/tillage/datasets/human/rna/recount3/adrenal_gland/GTEX-11GSP-0326-SM-5A5KW.1/coverage.w5 768 384 0.01 sum_sqrt 7525 RNA:adrenal_gland +7526 GTEX-13PVR-0226-SM-5RQJI.1 /home/drk/tillage/datasets/human/rna/recount3/adrenal_gland/GTEX-13PVR-0226-SM-5RQJI.1/coverage.w5 768 384 0.01 sum_sqrt 7526 RNA:adrenal_gland +7527 GTEX-14PKV-0726-SM-686ZF.1 /home/drk/tillage/datasets/human/rna/recount3/adrenal_gland/GTEX-14PKV-0726-SM-686ZF.1/coverage.w5 768 384 0.01 sum_sqrt 7527 RNA:adrenal_gland +7528 GTEX-T6MN-2226-SM-EVYAM.1 /home/drk/tillage/datasets/human/rna/recount3/bladder/GTEX-T6MN-2226-SM-EVYAM.1/coverage.w5 768 384 0.01 sum_sqrt 7528 RNA:bladder +7529 GTEX-U3ZN-1226-SM-4DXUD.1 /home/drk/tillage/datasets/human/rna/recount3/bladder/GTEX-U3ZN-1226-SM-4DXUD.1/coverage.w5 768 384 0.01 sum_sqrt 7529 RNA:bladder +7530 GTEX-U4B1-1226-SM-4DXT7.1 /home/drk/tillage/datasets/human/rna/recount3/bladder/GTEX-U4B1-1226-SM-4DXT7.1/coverage.w5 768 384 0.01 sum_sqrt 7530 RNA:bladder +7531 GTEX-1I4MK-0002-SM-EZ6M9.1 /home/drk/tillage/datasets/human/rna/recount3/blood/GTEX-1I4MK-0002-SM-EZ6M9.1/coverage.w5 768 384 0.01 sum_sqrt 7531 RNA:blood +7532 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K-562-SM-7LG4B.1 /home/drk/tillage/datasets/human/rna/recount3/bone_marrow/K-562-SM-7LG4B.1/coverage.w5 768 384 0.01 sum_sqrt 7538 RNA:bone_marrow +7539 GTEX-13FTY-0011-R11a-SM-5IJEA.1 /home/drk/tillage/datasets/human/rna/recount3/brain/GTEX-13FTY-0011-R11a-SM-5IJEA.1/coverage.w5 768 384 0.01 sum_sqrt 7539 RNA:brain +7540 GTEX-1EX96-0011-R4a-SM-ARU82.1 /home/drk/tillage/datasets/human/rna/recount3/brain/GTEX-1EX96-0011-R4a-SM-ARU82.1/coverage.w5 768 384 0.01 sum_sqrt 7540 RNA:brain +7541 GTEX-1H3O1-1726-SM-9WYSR.1 /home/drk/tillage/datasets/human/rna/recount3/brain/GTEX-1H3O1-1726-SM-9WYSR.1/coverage.w5 768 384 0.01 sum_sqrt 7541 RNA:brain +7542 GTEX-13W3W-1226-SM-5LU4H.1 /home/drk/tillage/datasets/human/rna/recount3/breast/GTEX-13W3W-1226-SM-5LU4H.1/coverage.w5 768 384 0.01 sum_sqrt 7542 RNA:breast +7543 GTEX-1GN1W-1926-SM-7P8TH.1 /home/drk/tillage/datasets/human/rna/recount3/breast/GTEX-1GN1W-1926-SM-7P8TH.1/coverage.w5 768 384 0.01 sum_sqrt 7543 RNA:breast +7544 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+7550 GTEX-ZAB4-2226-SM-5HL97.1 /home/drk/tillage/datasets/human/rna/recount3/colon/GTEX-ZAB4-2226-SM-5HL97.1/coverage.w5 768 384 0.01 sum_sqrt 7550 RNA:colon +7551 GTEX-14DAR-0726-SM-5RQIA.1 /home/drk/tillage/datasets/human/rna/recount3/esophagus/GTEX-14DAR-0726-SM-5RQIA.1/coverage.w5 768 384 0.01 sum_sqrt 7551 RNA:esophagus +7552 GTEX-1RAZR-1426-SM-EVR4M.1 /home/drk/tillage/datasets/human/rna/recount3/esophagus/GTEX-1RAZR-1426-SM-EVR4M.1/coverage.w5 768 384 0.01 sum_sqrt 7552 RNA:esophagus +7553 GTEX-ZDTT-1326-SM-4WKFH.1 /home/drk/tillage/datasets/human/rna/recount3/esophagus/GTEX-ZDTT-1326-SM-4WKFH.1/coverage.w5 768 384 0.01 sum_sqrt 7553 RNA:esophagus +7554 GTEX-PLZ4-2326-SM-EYYV5.1 /home/drk/tillage/datasets/human/rna/recount3/fallopian_tube/GTEX-PLZ4-2326-SM-EYYV5.1/coverage.w5 768 384 0.01 sum_sqrt 7554 RNA:fallopian_tube +7555 GTEX-S32W-1326-SM-4AD5Q.1 /home/drk/tillage/datasets/human/rna/recount3/fallopian_tube/GTEX-S32W-1326-SM-4AD5Q.1/coverage.w5 768 384 0.01 sum_sqrt 7555 RNA:fallopian_tube +7556 GTEX-T6MO-1026-SM-4DM72.1 /home/drk/tillage/datasets/human/rna/recount3/fallopian_tube/GTEX-T6MO-1026-SM-4DM72.1/coverage.w5 768 384 0.01 sum_sqrt 7556 RNA:fallopian_tube +7557 GTEX-11LCK-0826-SM-5PNYD.1 /home/drk/tillage/datasets/human/rna/recount3/heart/GTEX-11LCK-0826-SM-5PNYD.1/coverage.w5 768 384 0.01 sum_sqrt 7557 RNA:heart +7558 GTEX-18465-0926-SM-731AY.1 /home/drk/tillage/datasets/human/rna/recount3/heart/GTEX-18465-0926-SM-731AY.1/coverage.w5 768 384 0.01 sum_sqrt 7558 RNA:heart +7559 GTEX-1MUQO-1226-SM-E9TJK.1 /home/drk/tillage/datasets/human/rna/recount3/heart/GTEX-1MUQO-1226-SM-E9TJK.1/coverage.w5 768 384 0.01 sum_sqrt 7559 RNA:heart +7560 GTEX-13112-2126-SM-5GCO4.1 /home/drk/tillage/datasets/human/rna/recount3/kidney/GTEX-13112-2126-SM-5GCO4.1/coverage.w5 768 384 0.01 sum_sqrt 7560 RNA:kidney +7561 GTEX-17F96-1926-SM-7MGWY.1 /home/drk/tillage/datasets/human/rna/recount3/kidney/GTEX-17F96-1926-SM-7MGWY.1/coverage.w5 768 384 0.01 sum_sqrt 7561 RNA:kidney +7562 GTEX-ZVZP-0926-SM-5GIDB.1 /home/drk/tillage/datasets/human/rna/recount3/kidney/GTEX-ZVZP-0926-SM-5GIDB.1/coverage.w5 768 384 0.01 sum_sqrt 7562 RNA:kidney +7563 GTEX-11EQ9-0526-SM-5A5JZ.1 /home/drk/tillage/datasets/human/rna/recount3/liver/GTEX-11EQ9-0526-SM-5A5JZ.1/coverage.w5 768 384 0.01 sum_sqrt 7563 RNA:liver +7564 GTEX-1QP66-0226-SM-DPRXS.1 /home/drk/tillage/datasets/human/rna/recount3/liver/GTEX-1QP66-0226-SM-DPRXS.1/coverage.w5 768 384 0.01 sum_sqrt 7564 RNA:liver +7565 GTEX-ZYT6-0626-SM-5E45V.1 /home/drk/tillage/datasets/human/rna/recount3/liver/GTEX-ZYT6-0626-SM-5E45V.1/coverage.w5 768 384 0.01 sum_sqrt 7565 RNA:liver +7566 GTEX-1399S-1726-SM-5L3DI.1 /home/drk/tillage/datasets/human/rna/recount3/lung/GTEX-1399S-1726-SM-5L3DI.1/coverage.w5 768 384 0.01 sum_sqrt 7566 RNA:lung +7567 GTEX-14AS3-0926-SM-5TDD6.1 /home/drk/tillage/datasets/human/rna/recount3/lung/GTEX-14AS3-0926-SM-5TDD6.1/coverage.w5 768 384 0.01 sum_sqrt 7567 RNA:lung +7568 GTEX-14JG1-0926-SM-5YY8W.1 /home/drk/tillage/datasets/human/rna/recount3/lung/GTEX-14JG1-0926-SM-5YY8W.1/coverage.w5 768 384 0.01 sum_sqrt 7568 RNA:lung +7569 GTEX-13QJ3-0726-SM-5SI68.1 /home/drk/tillage/datasets/human/rna/recount3/muscle/GTEX-13QJ3-0726-SM-5SI68.1/coverage.w5 768 384 0.01 sum_sqrt 7569 RNA:muscle +7570 GTEX-14PJ4-2426-SM-6EU1U.1 /home/drk/tillage/datasets/human/rna/recount3/muscle/GTEX-14PJ4-2426-SM-6EU1U.1/coverage.w5 768 384 0.01 sum_sqrt 7570 RNA:muscle +7571 GTEX-1H1CY-2726-SM-9MQLR.1 /home/drk/tillage/datasets/human/rna/recount3/muscle/GTEX-1H1CY-2726-SM-9MQLR.1/coverage.w5 768 384 0.01 sum_sqrt 7571 RNA:muscle +7572 GTEX-14PJ6-2426-SM-6ETZS.1 /home/drk/tillage/datasets/human/rna/recount3/nerve/GTEX-14PJ6-2426-SM-6ETZS.1/coverage.w5 768 384 0.01 sum_sqrt 7572 RNA:nerve +7573 GTEX-1HKZK-0626-SM-ADEHP.1 /home/drk/tillage/datasets/human/rna/recount3/nerve/GTEX-1HKZK-0626-SM-ADEHP.1/coverage.w5 768 384 0.01 sum_sqrt 7573 RNA:nerve +7574 GTEX-11VI4-1026-SM-5EQM1.1 /home/drk/tillage/datasets/human/rna/recount3/ovary/GTEX-11VI4-1026-SM-5EQM1.1/coverage.w5 768 384 0.01 sum_sqrt 7574 RNA:ovary +7575 GTEX-1269C-1826-SM-5N9E1.1 /home/drk/tillage/datasets/human/rna/recount3/ovary/GTEX-1269C-1826-SM-5N9E1.1/coverage.w5 768 384 0.01 sum_sqrt 7575 RNA:ovary +7576 GTEX-1399S-2126-SM-5J2MH.1 /home/drk/tillage/datasets/human/rna/recount3/ovary/GTEX-1399S-2126-SM-5J2MH.1/coverage.w5 768 384 0.01 sum_sqrt 7576 RNA:ovary +7577 GTEX-11I78-0626-SM-5A5LZ.1 /home/drk/tillage/datasets/human/rna/recount3/pancreas/GTEX-11I78-0626-SM-5A5LZ.1/coverage.w5 768 384 0.01 sum_sqrt 7577 RNA:pancreas +7578 GTEX-14PJ6-0926-SM-686ZA.1 /home/drk/tillage/datasets/human/rna/recount3/pancreas/GTEX-14PJ6-0926-SM-686ZA.1/coverage.w5 768 384 0.01 sum_sqrt 7578 RNA:pancreas +7579 GTEX-1HKZK-1126-SM-9WG82.1 /home/drk/tillage/datasets/human/rna/recount3/pancreas/GTEX-1HKZK-1126-SM-9WG82.1/coverage.w5 768 384 0.01 sum_sqrt 7579 RNA:pancreas +7580 GTEX-12WSC-3126-SM-5GCNB.1 /home/drk/tillage/datasets/human/rna/recount3/pituitary/GTEX-12WSC-3126-SM-5GCNB.1/coverage.w5 768 384 0.01 sum_sqrt 7580 RNA:pituitary +7581 GTEX-145LS-3226-SM-5TDCA.1 /home/drk/tillage/datasets/human/rna/recount3/pituitary/GTEX-145LS-3226-SM-5TDCA.1/coverage.w5 768 384 0.01 sum_sqrt 7581 RNA:pituitary +7582 GTEX-1I1GR-3026-SM-ARU7C.1 /home/drk/tillage/datasets/human/rna/recount3/pituitary/GTEX-1I1GR-3026-SM-ARU7C.1/coverage.w5 768 384 0.01 sum_sqrt 7582 RNA:pituitary +7583 GTEX-11P82-1126-SM-5BC5K.1 /home/drk/tillage/datasets/human/rna/recount3/prostate/GTEX-11P82-1126-SM-5BC5K.1/coverage.w5 768 384 0.01 sum_sqrt 7583 RNA:prostate +7584 GTEX-1KXAM-1126-SM-E9TJU.1 /home/drk/tillage/datasets/human/rna/recount3/prostate/GTEX-1KXAM-1126-SM-E9TJU.1/coverage.w5 768 384 0.01 sum_sqrt 7584 RNA:prostate +7585 GTEX-P4PQ-2026-SM-E9U4E.1 /home/drk/tillage/datasets/human/rna/recount3/prostate/GTEX-P4PQ-2026-SM-E9U4E.1/coverage.w5 768 384 0.01 sum_sqrt 7585 RNA:prostate +7586 GTEX-1J8QM-1826-SM-A96TA.1 /home/drk/tillage/datasets/human/rna/recount3/salivary_gland/GTEX-1J8QM-1826-SM-A96TA.1/coverage.w5 768 384 0.01 sum_sqrt 7586 RNA:salivary_gland +7587 GTEX-YB5K-1726-SM-5IFIZ.1 /home/drk/tillage/datasets/human/rna/recount3/salivary_gland/GTEX-YB5K-1726-SM-5IFIZ.1/coverage.w5 768 384 0.01 sum_sqrt 7587 RNA:salivary_gland +7588 GTEX-ZLWG-2026-SM-DO11F.1 /home/drk/tillage/datasets/human/rna/recount3/salivary_gland/GTEX-ZLWG-2026-SM-DO11F.1/coverage.w5 768 384 0.01 sum_sqrt 7588 RNA:salivary_gland +7589 GTEX-133LE-2326-SM-5K7W3.1 /home/drk/tillage/datasets/human/rna/recount3/skin/GTEX-133LE-2326-SM-5K7W3.1/coverage.w5 768 384 0.01 sum_sqrt 7589 RNA:skin +7590 GTEX-139TS-0008-SM-62LDG.1 /home/drk/tillage/datasets/human/rna/recount3/skin/GTEX-139TS-0008-SM-62LDG.1/coverage.w5 768 384 0.01 sum_sqrt 7590 RNA:skin +7591 GTEX-13U4I-0126-SM-5LU38.1 /home/drk/tillage/datasets/human/rna/recount3/skin/GTEX-13U4I-0126-SM-5LU38.1/coverage.w5 768 384 0.01 sum_sqrt 7591 RNA:skin +7592 GTEX-14PJN-0826-SM-686ZL.1 /home/drk/tillage/datasets/human/rna/recount3/small_intestine/GTEX-14PJN-0826-SM-686ZL.1/coverage.w5 768 384 0.01 sum_sqrt 7592 RNA:small_intestine +7593 GTEX-1PDJ9-1826-SM-E9U66.1 /home/drk/tillage/datasets/human/rna/recount3/small_intestine/GTEX-1PDJ9-1826-SM-E9U66.1/coverage.w5 768 384 0.01 sum_sqrt 7593 RNA:small_intestine +7594 GTEX-ZF2S-1726-SM-57WFT.1 /home/drk/tillage/datasets/human/rna/recount3/small_intestine/GTEX-ZF2S-1726-SM-57WFT.1/coverage.w5 768 384 0.01 sum_sqrt 7594 RNA:small_intestine +7595 GTEX-14PJ4-0526-SM-6871G.1 /home/drk/tillage/datasets/human/rna/recount3/spleen/GTEX-14PJ4-0526-SM-6871G.1/coverage.w5 768 384 0.01 sum_sqrt 7595 RNA:spleen +7596 GTEX-15DYW-1426-SM-6LPIW.1 /home/drk/tillage/datasets/human/rna/recount3/spleen/GTEX-15DYW-1426-SM-6LPIW.1/coverage.w5 768 384 0.01 sum_sqrt 7596 RNA:spleen +7597 GTEX-1F75I-0226-SM-7MKHQ.1 /home/drk/tillage/datasets/human/rna/recount3/spleen/GTEX-1F75I-0226-SM-7MKHQ.1/coverage.w5 768 384 0.01 sum_sqrt 7597 RNA:spleen +7598 GTEX-1399U-1626-SM-5P9J3.1 /home/drk/tillage/datasets/human/rna/recount3/stomach/GTEX-1399U-1626-SM-5P9J3.1/coverage.w5 768 384 0.01 sum_sqrt 7598 RNA:stomach +7599 GTEX-14PKV-1826-SM-69LO9.1 /home/drk/tillage/datasets/human/rna/recount3/stomach/GTEX-14PKV-1826-SM-69LO9.1/coverage.w5 768 384 0.01 sum_sqrt 7599 RNA:stomach +7600 GTEX-1IDJU-1526-SM-CNNR3.1 /home/drk/tillage/datasets/human/rna/recount3/stomach/GTEX-1IDJU-1526-SM-CNNR3.1/coverage.w5 768 384 0.01 sum_sqrt 7600 RNA:stomach +7601 GTEX-1KD5A-1826-SM-DHXJI.1 /home/drk/tillage/datasets/human/rna/recount3/testis/GTEX-1KD5A-1826-SM-DHXJI.1/coverage.w5 768 384 0.01 sum_sqrt 7601 RNA:testis +7602 GTEX-1MA7X-1526-SM-DHXJF.1 /home/drk/tillage/datasets/human/rna/recount3/testis/GTEX-1MA7X-1526-SM-DHXJF.1/coverage.w5 768 384 0.01 sum_sqrt 7602 RNA:testis +7603 GTEX-13FH7-0126-SM-5KLZ1.1 /home/drk/tillage/datasets/human/rna/recount3/thyroid/GTEX-13FH7-0126-SM-5KLZ1.1/coverage.w5 768 384 0.01 sum_sqrt 7603 RNA:thyroid +7604 GTEX-15CHQ-0826-SM-69LOT.1 /home/drk/tillage/datasets/human/rna/recount3/thyroid/GTEX-15CHQ-0826-SM-69LOT.1/coverage.w5 768 384 0.01 sum_sqrt 7604 RNA:thyroid +7605 GTEX-1J1OQ-0526-SM-A9G2P.1 /home/drk/tillage/datasets/human/rna/recount3/thyroid/GTEX-1J1OQ-0526-SM-A9G2P.1/coverage.w5 768 384 0.01 sum_sqrt 7605 RNA:thyroid +7606 GTEX-13FTX-1026-SM-5J2O5.1 /home/drk/tillage/datasets/human/rna/recount3/uterus/GTEX-13FTX-1026-SM-5J2O5.1/coverage.w5 768 384 0.01 sum_sqrt 7606 RNA:uterus +7607 GTEX-1MA7W-1526-SM-DHXKS.1 /home/drk/tillage/datasets/human/rna/recount3/uterus/GTEX-1MA7W-1526-SM-DHXKS.1/coverage.w5 768 384 0.01 sum_sqrt 7607 RNA:uterus +7608 GTEX-11EMC-1926-SM-5A5JU.1 /home/drk/tillage/datasets/human/rna/recount3/vagina/GTEX-11EMC-1926-SM-5A5JU.1/coverage.w5 768 384 0.01 sum_sqrt 7608 RNA:vagina +7609 GTEX-12WSB-2426-SM-5EGJC.1 /home/drk/tillage/datasets/human/rna/recount3/vagina/GTEX-12WSB-2426-SM-5EGJC.1/coverage.w5 768 384 0.01 sum_sqrt 7609 RNA:vagina +7610 GTEX-W5WG-1026-SM-4LMIF.1 /home/drk/tillage/datasets/human/rna/recount3/vagina/GTEX-W5WG-1026-SM-4LMIF.1/coverage.w5 768 384 0.01 sum_sqrt 7610 RNA:vagina diff --git a/pyproject.toml b/pyproject.toml index 52f16d5..bd28622 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,27 +1,50 @@ [build-system] -requires = [ - "setuptools>=45", - "wheel", - "setuptools_scm>=6.2" -] +requires = ["setuptools>=69.0.3", "setuptools_scm>=8.0.4"] build-backend = "setuptools.build_meta" [project] name = "borzoi" +description = "borzoi" authors = [ {name = "David Kelley", email = "drk@calicolabs.com"}, {name = "Johannes Linder", email = "jlinder@calicolabs.com"} ] readme = "README.md" -requires-python = ">=3.8, <3.11" classifiers = ["License :: OSI Approved :: Apache License"] -dynamic = ["version", "description"] +dynamic = ["version"] + +requires-python = ">=3.9" +dependencies = [ + "h5py~=3.10.0", + "intervaltree~=3.1.0", + "joblib~=1.1.1", + "matplotlib~=3.7.1", + "google-cloud-storage~=2.0.0", + "natsort~=7.1.1", + "networkx~=2.8.4", + "numpy~=1.24.3", + "pandas~=1.5.3", + "pybigwig~=0.3.18", + "pybedtools~=0.10.0", + "pysam~=0.22.0", + "qnorm~=0.8.1", + "seaborn~=0.12.2", + "scikit-learn~=1.2.2", + "scipy~=1.9.1", + "tensorflow~=2.15.0", + "tqdm~=4.65.0", + "pyfaidx~=0.7.1", + "pyranges~=0.0.129", +] [project.optional-dependencies] dev = [ - "black==22.3.0", - "pytest==7.1.2" + "black~=23.12.1", + "pytest~=7.4.4", + "ruff~=0.1.11", ] -[tool.setuptools_scm] +[project.urls] +Homepage = "https://github.com/calico/borzoi" +[tool.setuptools_scm] \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 5c596bb..0000000 --- a/setup.cfg +++ /dev/null @@ -1,43 +0,0 @@ -[metadata] -name = borzoi -author = David Kelley -author_email = drk@calicolabs.com -description = Machine learning methods for DNA sequence analysis. -long_description = file: README.md -long_description_content_type = text/markdown -url = https://github.com/calico/borzoi -project_urls = - Bug Tracker = https://github.com/calico/borzoi/issues -classifiers = - Programming Language :: Python :: 3 - License :: OSI Approved :: Apache License - Operating System :: OS Independent - -[options] -package_dir = - = src -packages = find: -python_requires = >=3.8, <3.11 -install_requires = - h5py~=3.7.0 - intervaltree~=3.1.0 - matplotlib~=3.7.1 - numpy~=1.24.3 - pandas~=1.5.3 - pybigwig~=0.3.18 - pysam~=0.21.0 - pybedtools~=0.9.0 - seaborn~=0.12.2 - scikit-learn~=1.2.2 - scipy~=1.9.1 - tensorflow~=2.12.0 - pyfaidx~=0.7.1 -# baskerville==0.0.1 - -[options.extras_require] -dev = - black==22.3.0 - pytest==7.1.2 - -[options.packages.find] -where = src diff --git a/src/scripts/borzoi_bench_crispr.py b/src/scripts/_archive/borzoi_bench_crispr.py similarity index 100% rename from src/scripts/borzoi_bench_crispr.py rename to src/scripts/_archive/borzoi_bench_crispr.py diff --git a/src/scripts/borzoi_bench_crispr_folds.py b/src/scripts/_archive/borzoi_bench_crispr_folds.py similarity index 100% rename from src/scripts/borzoi_bench_crispr_folds.py rename to src/scripts/_archive/borzoi_bench_crispr_folds.py diff --git a/src/scripts/borzoi_bench_flowfish_folds.py b/src/scripts/_archive/borzoi_bench_flowfish_folds.py similarity index 100% rename from src/scripts/borzoi_bench_flowfish_folds.py rename to src/scripts/_archive/borzoi_bench_flowfish_folds.py diff --git a/src/scripts/borzoi_bench_gasperini_folds.py b/src/scripts/_archive/borzoi_bench_gasperini_folds.py similarity index 100% rename from src/scripts/borzoi_bench_gasperini_folds.py rename to src/scripts/_archive/borzoi_bench_gasperini_folds.py diff --git a/src/scripts/_archive/borzoi_satg_gene.py b/src/scripts/_archive/borzoi_satg_gene.py new file mode 100755 index 0000000..eb3c5c6 --- /dev/null +++ b/src/scripts/_archive/borzoi_satg_gene.py @@ -0,0 +1,351 @@ +#!/usr/bin/env python +# Copyright 2022 Calico LLC +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# ========================================================================= +from optparse import OptionParser + +import gc +import json +import os +import pickle + +import h5py +import numpy as np +import pandas as pd +import pysam + +from baskerville.dataset import targets_prep_strand +from baskerville import dna_io +from baskerville import gene as bgene +from baskerville import seqnn + +""" +borzoi_satg_gene.py + +Perform a gradient saliency analysis for genes specified in a GTF file. +""" + +################################################################################ +# main +################################################################################ +def main(): + usage = "usage: %prog [options] " + parser = OptionParser(usage) + parser.add_option( + "-f", + dest="genome_fasta", + default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + help="Genome FASTA for sequences [Default: %default]", + ) + parser.add_option( + "-o", + dest="out_dir", + default="satg_out", + help="Output directory [Default: %default]", + ) + parser.add_option( + "-p", + dest="processes", + default=None, + type="int", + help="Number of processes, passed by multi script", + ) + parser.add_option( + "--rc", + dest="rc", + default=False, + action="store_true", + help="Ensemble forward and reverse complement predictions [Default: %default]", + ) + parser.add_option( + "--shifts", + dest="shifts", + default="0", + type="str", + help="Ensemble prediction shifts [Default: %default]", + ) + parser.add_option( + "--span", + dest="span", + default=False, + action="store_true", + help="Aggregate entire gene span [Default: %default]", + ) + parser.add_option( + "--sum", + dest="sum_targets", + default=False, + action="store_true", + help="Sum targets for single output [Default: %default]", + ) + parser.add_option( + "-t", + dest="targets_file", + default=None, + type="str", + help="File specifying target indexes and labels in table format", + ) + (options, args) = parser.parse_args() + + if len(args) == 3: + # single worker + params_file = args[0] + model_file = args[1] + genes_gtf_file = args[2] + + elif len(args) == 4: + # master script + options_pkl_file = args[0] + params_file = args[1] + model_file = args[2] + genes_gtf_file = args[3] + + # load options + options_pkl = open(options_pkl_file, "rb") + options = pickle.load(options_pkl) + options_pkl.close() + + elif len(args) == 5: + # multi worker + options_pkl_file = args[0] + params_file = args[1] + model_file = args[2] + genes_gtf_file = args[3] + worker_index = int(args[4]) + + # load options + options_pkl = open(options_pkl_file, "rb") + options = pickle.load(options_pkl) + options_pkl.close() + + # update output directory + options.out_dir = "%s/job%d" % (options.out_dir, worker_index) + + else: + parser.error("Must provide parameter and model files and BED file") + + if not os.path.isdir(options.out_dir): + os.mkdir(options.out_dir) + + options.shifts = [int(shift) for shift in options.shifts.split(",")] + + ################################################################# + # read parameters and targets + + # read model parameters + with open(params_file) as params_open: + params = json.load(params_open) + params_model = params["model"] + params_train = params["train"] + seq_len = params_model["seq_length"] + + if options.targets_file is None: + parser.error("Must provide targets table to properly handle strands.") + else: + targets_df = pd.read_csv(options.targets_file, sep="\t", index_col=0) + + # prep strand + orig_new_index = dict(zip(targets_df.index, np.arange(targets_df.shape[0]))) + targets_strand_pair = np.array( + [orig_new_index[ti] for ti in targets_df.strand_pair] + ) + targets_strand_df = targets_prep_strand(targets_df) + num_targets = targets_strand_df.shape[0] + if options.sum_targets: + num_targets = 1 + + # params strand_pair unnecessary because I'm not building ensemble in graph + + ################################################################# + # setup model + + seqnn_model = seqnn.SeqNN(params_model) + seqnn_model.restore(model_file) + seqnn_model.build_slice(targets_df.index, options.sum_targets) + + model_stride = seqnn_model.model_strides[0] + model_crop = seqnn_model.target_crops[0] + target_length = seqnn_model.target_lengths[0] + + ################################################################# + # read genes + + # parse GTF + transcriptome = bgene.Transcriptome(genes_gtf_file) + + # order valid genes + genome_open = pysam.Fastafile(options.genome_fasta) + gene_list = sorted(transcriptome.genes.keys()) + num_genes = len(gene_list) + + # filter for worker genes + if options.processes is not None: + # determine boundaries + worker_bounds = np.linspace(0, num_genes, options.processes + 1, dtype="int") + worker_start = worker_bounds[worker_index] + worker_end = worker_bounds[worker_index + 1] + gene_list = [gene_list[gi] for gi in range(worker_start, worker_end)] + num_genes = len(gene_list) + + ################################################################# + # setup output + + min_start = -model_stride * model_crop + + # choose gene sequences + genes_chr = [] + genes_start = [] + genes_end = [] + genes_strand = [] + for gene_id in gene_list: + gene = transcriptome.genes[gene_id] + genes_chr.append(gene.chrom) + genes_strand.append(gene.strand) + + gene_midpoint = gene.midpoint() + gene_start = max(min_start, gene_midpoint - seq_len // 2) + gene_end = gene_start + seq_len + genes_start.append(gene_start) + genes_end.append(gene_end) + + # initialize HDF5 + scores_h5_file = "%s/scores.h5" % options.out_dir + if os.path.isfile(scores_h5_file): + os.remove(scores_h5_file) + scores_h5 = h5py.File(scores_h5_file, "w") + scores_h5.create_dataset("seqs", dtype="bool", shape=(num_genes, seq_len, 4)) + scores_h5.create_dataset( + "grads", dtype="float16", shape=(num_genes, seq_len, 4, num_targets) + ) + scores_h5.create_dataset("gene", data=np.array(gene_list, dtype="S")) + scores_h5.create_dataset("chr", data=np.array(genes_chr, dtype="S")) + scores_h5.create_dataset("start", data=np.array(genes_start)) + scores_h5.create_dataset("end", data=np.array(genes_end)) + scores_h5.create_dataset("strand", data=np.array(genes_strand, dtype="S")) + + ################################################################# + # predict scores, write output + + for gi, gene_id in enumerate(gene_list): + print("Predicting %d, %s" % (gi, gene_id), flush=True) + gene = transcriptome.genes[gene_id] + + # make sequence + seq_1hot = make_seq_1hot( + genome_open, genes_chr[gi], genes_start[gi], genes_end[gi], seq_len + ) + + # determine output sequence start + seq_out_start = genes_start[gi] + model_stride * model_crop + seq_out_len = model_stride * target_length + + # determine output positions + gene_slice = gene.output_slice( + seq_out_start, seq_out_len, model_stride, options.span + ) + if options.rc: + gene_slice_rc = target_length - gene_slice - 1 + + if len(gene_slice) == 0: + print("WARNING: %s no gene positions found." % gene_id) + grads = np.zeros((seq_len, 4, num_targets), dtype="float16") + + else: + grads_ens = [] + for shift in options.shifts: + seq_1hot_aug = dna_io.hot1_augment(seq_1hot, shift=shift) + grads_aug = seqnn_model.gradients(seq_1hot_aug, pos_slice=gene_slice) + grads_aug = unaugment_grads(grads_aug, fwdrc=True, shift=shift) + grads_ens.append(grads_aug) + + if options.rc: + seq_1hot_aug = dna_io.hot1_rc(seq_1hot_aug) + grads_aug = seqnn_model.gradients( + seq_1hot_aug, pos_slice=gene_slice_rc + ) + grads_aug = unaugment_grads(grads_aug, fwdrc=False, shift=shift) + grads_aug = grads_aug[..., targets_strand_pair] + grads_ens.append(grads_aug) + + # ensemble mean + grads = np.array(grads_ens).mean(axis=0) + + # slice relevant strand targets + if genes_strand[gi] == "+": + gene_strand_mask = targets_df.strand != "-" + else: + gene_strand_mask = targets_df.strand != "+" + grads = grads[..., gene_strand_mask] + + # write to HDF5 + scores_h5["seqs"][gi] = seq_1hot + scores_h5["grads"][gi] = grads + + gc.collect() + + # close files + genome_open.close() + scores_h5.close() + + +def unaugment_grads(grads, fwdrc=False, shift=0): + """Undo sequence augmentation.""" + # reverse complement + if not fwdrc: + # reverse + grads = grads[::-1, :, :] + + # swap A and T + grads[:, [0, 3], :] = grads[:, [3, 0], :] + + # swap C and G + grads[:, [1, 2], :] = grads[:, [2, 1], :] + + # undo shift + if shift < 0: + # shift sequence right + grads[-shift:, :, :] = grads[:shift, :, :] + + # fill in left unknowns + grads[:-shift, :, :] = 0 + + elif shift > 0: + # shift sequence left + grads[:-shift, :, :] = grads[shift:, :, :] + + # fill in right unknowns + grads[-shift:, :, :] = 0 + + return grads + + +def make_seq_1hot(genome_open, chrm, start, end, seq_len): + if start < 0: + seq_dna = "N" * (-start) + genome_open.fetch(chrm, 0, end) + else: + seq_dna = genome_open.fetch(chrm, start, end) + + # extend to full length + if len(seq_dna) < seq_len: + seq_dna += "N" * (seq_len - len(seq_dna)) + + seq_1hot = dna_io.dna_1hot(seq_dna) + return seq_1hot + + +################################################################################ +# __main__ +################################################################################ +if __name__ == "__main__": + main() diff --git a/src/scripts/borzoi_satg_gene_multi.py b/src/scripts/_archive/borzoi_satg_gene_multi.py similarity index 100% rename from src/scripts/borzoi_satg_gene_multi.py rename to src/scripts/_archive/borzoi_satg_gene_multi.py diff --git a/src/scripts/basenji_bench_classify.py b/src/scripts/borzoi_bench_classify.py old mode 100644 new mode 100755 similarity index 99% rename from src/scripts/basenji_bench_classify.py rename to src/scripts/borzoi_bench_classify.py index 5df06e9..2e8a5a4 --- a/src/scripts/basenji_bench_classify.py +++ b/src/scripts/borzoi_bench_classify.py @@ -17,7 +17,7 @@ import seaborn as sns ''' -basenji_bench_classify.py +borzoi_bench_classify.py ''' ################################################################################ diff --git a/src/scripts/basenji_bench_gtex_folds.py b/src/scripts/borzoi_bench_gtex_folds_sad.py old mode 100644 new mode 100755 similarity index 96% rename from src/scripts/basenji_bench_gtex_folds.py rename to src/scripts/borzoi_bench_gtex_folds_sad.py index 4ea5110..17211d7 --- a/src/scripts/basenji_bench_gtex_folds.py +++ b/src/scripts/borzoi_bench_gtex_folds_sad.py @@ -29,9 +29,9 @@ import slurm """ -basenji_bench_gtex_folds.py +borzoi_bench_gtex_folds_sad.py -Benchmark Basenji model replicates on GTEx eQTL classification task. +Benchmark Borzoi model replicates on GTEx eQTL classification task (gene-agnostic). """ ################################################################################ @@ -42,11 +42,11 @@ def main(): parser = OptionParser(usage) # sad options - sad_options = OptionGroup(parser, 'basenji_sad.py options') + sad_options = OptionGroup(parser, 'borzoi_sad.py options') sad_options.add_option( '-f', dest='genome_fasta', - default='%s/assembly/ucsc/hg38.fa' % os.environ['HG38'], + default='%s/assembly/ucsc/hg38.fa' % os.environ.get('BORZOI_HG38', 'hg38'), help='Genome FASTA for sequences [Default: %default]' ) sad_options.add_option( @@ -117,7 +117,7 @@ def main(): parser.add_option_group(sad_options) # classify - class_options = OptionGroup(parser, 'basenji_bench_classify.py options') + class_options = OptionGroup(parser, 'borzoi_bench_classify.py options') class_options.add_option( '--cn', dest='class_name', @@ -179,6 +179,11 @@ def main(): dest='gtex_vcf_dir', default='/home/drk/seqnn/data/gtex_fine/susie_pip90' ) + fold_options.add_option( + '--susie', + dest='susie_dir', + default='/home/drk/seqnn/data/gtex_fine/tissues_susie', + ) fold_options.add_option( '--name', dest='name', @@ -243,8 +248,8 @@ def main(): # SAD # SAD command base - cmd_base = '. /home/jlinder/anaconda3/etc/profile.d/conda.sh;' - cmd_base += ' conda activate %s;' % options.conda_env + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += 'conda activate %s;' % options.conda_env cmd_base += ' echo $HOSTNAME;' jobs = [] @@ -275,7 +280,7 @@ def main(): options_pkl.close() # create base fold command - cmd_fold = '%s time basenji_sad.py %s %s %s' % ( + cmd_fold = '%s time borzoi_sad.py %s %s %s' % ( cmd_base, options_pkl_file, params_file, model_file) for pi in range(options.processes): @@ -302,7 +307,7 @@ def main(): options_pkl.close() # create base fold command - cmd_fold = '%s time basenji_sad.py %s %s %s' % ( + cmd_fold = '%s time borzoi_sad.py %s %s %s' % ( cmd_base, options_pkl_file, params_file, model_file) for pi in range(options.processes): @@ -399,7 +404,7 @@ def main(): # fit classifiers ################################################################ - cmd_base = 'basenji_bench_classify.py -i 100 -p 2 -r 44 -s' + cmd_base = 'borzoi_bench_classify.py -i 100 -p 2 -r 44 -s' cmd_base += ' --msl %d' % options.msl if options.class_targets_file is not None: @@ -451,7 +456,7 @@ def main(): ################################################################ # coefficient analysis - cmd_base = 'basenji_gtex_coef.py -g %s' % options.gtex_vcf_dir + cmd_base = 'borzoi_gtex_coef_sad.py -g %s --susie %s' % (options.gtex_vcf_dir, options.susie_dir) jobs = [] for ci in range(options.crosses): diff --git a/src/scripts/borzoi_bench_gtex_folds.py b/src/scripts/borzoi_bench_gtex_folds_sed.py old mode 100644 new mode 100755 similarity index 97% rename from src/scripts/borzoi_bench_gtex_folds.py rename to src/scripts/borzoi_bench_gtex_folds_sed.py index a3f3c81..c762b28 --- a/src/scripts/borzoi_bench_gtex_folds.py +++ b/src/scripts/borzoi_bench_gtex_folds_sed.py @@ -29,9 +29,9 @@ import slurm """ -borzoi_bench_gtex_folds.py +borzoi_bench_gtex_folds_sed.py -Benchmark Borzoi model replicates on GTEx eQTL coefficient task. +Benchmark Borzoi model replicates on GTEx eQTL coefficient task (gene-specific). """ ################################################################################ @@ -53,13 +53,13 @@ def main(): sed_options.add_option( '-f', dest='genome_fasta', - default='%s/assembly/ucsc/hg38.fa' % os.environ['HG38'], + default='%s/assembly/ucsc/hg38.fa' % os.environ.get('BORZOI_HG38', 'hg38'), help='Genome FASTA for sequences [Default: %default]', ) sed_options.add_option( '-g', dest='genes_gtf', - default='%s/genes/gencode41/gencode41_basic_nort.gtf' % os.environ['HG38'], + default='%s/genes/gencode41/gencode41_basic_nort.gtf' % os.environ.get('BORZOI_HG38', 'hg38'), help='GTF for gene definition [Default %default]', ) sed_options.add_option( @@ -156,6 +156,11 @@ def main(): dest='gtex_vcf_dir', default='/home/drk/seqnn/data/gtex_fine/susie_pip90', ) + fold_options.add_option( + '--susie', + dest='susie_dir', + default='/home/drk/seqnn/data/gtex_fine/tissues_susie', + ) fold_options.add_option( '--name', dest='name', @@ -220,8 +225,8 @@ def main(): # SED # SED command base - cmd_base = '. /home/drk/anaconda3/etc/profile.d/conda.sh;' - cmd_base += ' conda activate %s;' % options.conda_env + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += 'conda activate %s;' % options.conda_env cmd_base += ' echo $HOSTNAME;' jobs = [] @@ -376,7 +381,7 @@ def main(): ################################################################ # coefficient analysis - cmd_base = 'borzoi_gtex_coef.py -g %s' % options.gtex_vcf_dir + cmd_base = 'borzoi_gtex_coef_sed.py -g %s --susie %s' % (options.gtex_vcf_dir, options.susie_dir) jobs = [] for ci in range(options.crosses): diff --git a/src/scripts/borzoi_bench_ipaqtl_folds.py b/src/scripts/borzoi_bench_ipaqtl_folds.py index 9ddc9af..b7efb66 100755 --- a/src/scripts/borzoi_bench_ipaqtl_folds.py +++ b/src/scripts/borzoi_bench_ipaqtl_folds.py @@ -41,19 +41,20 @@ def main(): sed_options.add_option( "-f", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) sed_options.add_option( "-g", dest="genes_gtf", - default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ["HG38"], + default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ.get('BORZOI_HG38', 'hg38'), help="GTF for gene definition [Default %default]", ) sed_options.add_option( "--apafile", dest="apa_file", - default="polyadb_human_v3.csv.gz" + default="%s/genes/polyadb/polyadb_human_v3.csv.gz" % os.environ.get('BORZOI_HG38', 'hg38'), + help="Csv for polya site definition [Default %default]", ) sed_options.add_option( "-o", @@ -236,8 +237,8 @@ def main(): # SNP scores # command base - cmd_base = ". /home/drk/anaconda3/etc/profile.d/conda.sh;" - cmd_base += " conda activate %s;" % options.conda_env + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += "conda activate %s;" % options.conda_env cmd_base += " echo $HOSTNAME;" jobs = [] @@ -370,7 +371,7 @@ def main(): cmd_base += " conda activate %s;" % options.conda_env cmd_base += " echo $HOSTNAME;" - cmd_base += " basenji_bench_classify.py -i 100 -p 2 -r 44 -s --stat COVR" + cmd_base += " borzoi_bench_classify.py -i 100 -p 2 -r 44 -s --stat COVR" cmd_base += " --msl %d" % options.msl jobs = [] diff --git a/src/scripts/borzoi_bench_paqtl_folds.py b/src/scripts/borzoi_bench_paqtl_folds.py index 9fc97c5..46697ff 100755 --- a/src/scripts/borzoi_bench_paqtl_folds.py +++ b/src/scripts/borzoi_bench_paqtl_folds.py @@ -41,19 +41,20 @@ def main(): sed_options.add_option( "-f", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) sed_options.add_option( "-g", dest="genes_gtf", - default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ["HG38"], + default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ.get('BORZOI_HG38', 'hg38'), help="GTF for gene definition [Default %default]", ) sed_options.add_option( "--apafile", dest="apa_file", - default="polyadb_human_v3.csv.gz" + default="%s/genes/polyadb/polyadb_human_v3.csv.gz" % os.environ.get('BORZOI_HG38', 'hg38'), + help="Csv for polya site definition [Default %default]", ) sed_options.add_option( "-o", @@ -236,8 +237,8 @@ def main(): # SNP scores # command base - cmd_base = ". /home/drk/anaconda3/etc/profile.d/conda.sh;" - cmd_base += " conda activate %s;" % options.conda_env + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += "conda activate %s;" % options.conda_env cmd_base += " echo $HOSTNAME;" jobs = [] @@ -370,7 +371,7 @@ def main(): cmd_base += " conda activate %s;" % options.conda_env cmd_base += " echo $HOSTNAME;" - cmd_base += " basenji_bench_classify.py -i 100 -p 2 -r 44 -s --stat COVR" + cmd_base += " borzoi_bench_classify.py -i 100 -p 2 -r 44 -s --stat COVR" cmd_base += " --msl %d" % options.msl jobs = [] diff --git a/src/scripts/borzoi_bench_sqtl_folds.py b/src/scripts/borzoi_bench_sqtl_folds.py index 6c74788..90d1237 100755 --- a/src/scripts/borzoi_bench_sqtl_folds.py +++ b/src/scripts/borzoi_bench_sqtl_folds.py @@ -41,14 +41,14 @@ def main(): sed_options.add_option( "-f", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) sed_options.add_option( "-g", dest="genes_gtf", - default="%s/genes/gencode41/gencode41_basic_nort_protein.gtf" - % os.environ["HG38"], + default="%s/genes/gencode41/gencode41_basic_nort.gtf" + % os.environ.get('BORZOI_HG38', 'hg38'), help="GTF for gene definition [Default %default]", ) sed_options.add_option( @@ -223,8 +223,8 @@ def main(): # SNP scores # command base - cmd_base = ". /home/drk/anaconda3/etc/profile.d/conda.sh;" - cmd_base += " conda activate %s;" % options.conda_env + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += "conda activate %s;" % options.conda_env cmd_base += " echo $HOSTNAME;" jobs = [] @@ -360,7 +360,7 @@ def main(): cmd_base += " conda activate %s;" % options.conda_env cmd_base += " echo $HOSTNAME;" - cmd_base += " basenji_bench_classify.py -i 100 -p 2 -r 44 -s --stat nDi" + cmd_base += " borzoi_bench_classify.py -i 100 -p 2 -r 44 -s --stat nDi" cmd_base += " --msl %d" % options.msl jobs = [] diff --git a/src/scripts/borzoi_bench_trip_folds.py b/src/scripts/borzoi_bench_trip_folds.py index 7a8e3ca..bcc2dd6 100755 --- a/src/scripts/borzoi_bench_trip_folds.py +++ b/src/scripts/borzoi_bench_trip_folds.py @@ -36,7 +36,7 @@ def main(): trip_options.add_option( "-f", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) trip_options.add_option( @@ -184,8 +184,8 @@ def main(): # TRIP prediction jobs # command base - cmd_base = ". /home/drk/anaconda3/etc/profile.d/conda.sh;" - cmd_base += " conda activate %s;" % options.conda_env + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += "conda activate %s;" % options.conda_env cmd_base += " echo $HOSTNAME;" jobs = [] diff --git a/src/scripts/basenji_gtex_coef.py b/src/scripts/borzoi_gtex_coef_sad.py old mode 100644 new mode 100755 similarity index 96% rename from src/scripts/basenji_gtex_coef.py rename to src/scripts/borzoi_gtex_coef_sad.py index 264c750..64ee40a --- a/src/scripts/basenji_gtex_coef.py +++ b/src/scripts/borzoi_gtex_coef_sad.py @@ -15,7 +15,7 @@ import seaborn as sns ''' -basenji_gtex_coef.py +borzoi_gtex_coef_sad.py Evaluate concordance of variant effect prediction sign classifcation and coefficient correlations (gene-agnostic). @@ -37,9 +37,15 @@ def main(): parser.add_option( '-g', dest='gtex_vcf_dir', - default='/home/drk/seqnn/data/gtex_fine/susie_pip90', + default='susie_pip90', help='GTEx VCF directory' ) + parser.add_option( + '--susie', + dest='susie_dir', + default='susie_pip90', + help='SuSiE directory' + ) parser.add_option( '-m', dest='min_variants', @@ -114,7 +120,7 @@ def main(): if options.verbose: print(tissue) # read causal variants - eqtl_df = read_eqtl(tissue, options.gtex_vcf_dir) + eqtl_df = read_eqtl(tissue, options.gtex_vcf_dir, susie_dir=options.susie_dir) if eqtl_df is not None and eqtl_df.shape[0] > options.min_variants: # read model predictions gtex_scores_file = f'{gtex_dir}/{tissue}_pos/sad.h5' @@ -180,7 +186,7 @@ def main(): print('Class AUROC: %.4f' % np.mean(metrics_df.auroc_class)) -def read_eqtl(tissue: str, gtex_vcf_dir: str, pip_t: float=0.9): +def read_eqtl(tissue: str, gtex_vcf_dir: str, pip_t: float=0.9, susie_dir: str='tissues_susie'): """Reads eQTLs from SUSIE output. Args: @@ -191,7 +197,6 @@ def read_eqtl(tissue: str, gtex_vcf_dir: str, pip_t: float=0.9): Returns: eqtl_df (pd.DataFrame): eQTL dataframe, or None if tissue skipped. """ - susie_dir = '/home/drk/seqnn/data/gtex_fine/tissues_susie' # read causal variants eqtl_file = f'{susie_dir}/{tissue}.tsv' diff --git a/src/scripts/borzoi_gtex_coef.py b/src/scripts/borzoi_gtex_coef_sed.py old mode 100644 new mode 100755 similarity index 97% rename from src/scripts/borzoi_gtex_coef.py rename to src/scripts/borzoi_gtex_coef_sed.py index b44d548..d9a4459 --- a/src/scripts/borzoi_gtex_coef.py +++ b/src/scripts/borzoi_gtex_coef_sed.py @@ -15,7 +15,7 @@ import seaborn as sns ''' -borzoi_gtex_coef.py +borzoi_gtex_coef_sed.py Evaluate concordance of variant effect prediction sign classifcation and coefficient correlations (gene-specific). @@ -37,9 +37,15 @@ def main(): parser.add_option( '-g', dest='gtex_vcf_dir', - default='/home/drk/seqnn/data/gtex_fine/susie_pip90', + default='susie_pip90', help='GTEx VCF directory', ) + parser.add_option( + '--susie', + dest='susie_dir', + default='susie_pip90', + help='SuSiE directory' + ) parser.add_option( '-m', dest='min_variants', @@ -138,7 +144,7 @@ def main(): if options.verbose: print(tissue) # read causal variants - eqtl_df = read_eqtl(tissue, options.gtex_vcf_dir) + eqtl_df = read_eqtl(tissue, options.gtex_vcf_dir, susie_dir=options.susie_dir) if eqtl_df is not None and eqtl_df.shape[0] > options.min_variants: # read model predictions @@ -203,7 +209,7 @@ def main(): print('Class AUROC: %.4f' % np.mean(metrics_df.auroc_class)) -def read_eqtl(tissue: str, gtex_vcf_dir: str, pip_t: float=0.9): +def read_eqtl(tissue: str, gtex_vcf_dir: str, pip_t: float=0.9, susie_dir: str='tissues_susie'): """Reads eQTLs from SUSIE output. Args: @@ -214,7 +220,6 @@ def read_eqtl(tissue: str, gtex_vcf_dir: str, pip_t: float=0.9): Returns: eqtl_df (pd.DataFrame): eQTL dataframe, or None if tissue skipped. """ - susie_dir = '/home/drk/seqnn/data/gtex_fine/tissues_susie' # read causal variants eqtl_file = f'{susie_dir}/{tissue}.tsv' diff --git a/src/scripts/basenji_sad.py b/src/scripts/borzoi_sad.py old mode 100644 new mode 100755 similarity index 99% rename from src/scripts/basenji_sad.py rename to src/scripts/borzoi_sad.py index d832139..2c12782 --- a/src/scripts/basenji_sad.py +++ b/src/scripts/borzoi_sad.py @@ -38,7 +38,7 @@ from baskerville import vcf as bvcf ''' -basenji_sad.py +borzoi_sad.py Compute SNP Activity Difference (SAD) scores for SNPs in a VCF file. ''' @@ -52,7 +52,7 @@ def main(): parser.add_option( '-f', dest='genome_fasta', - default='%s/assembly/ucsc/hg38.fa' % os.environ["HG38"], + default='%s/assembly/ucsc/hg38.fa' % os.environ.get('BORZOI_HG38', 'hg38'), help='Genome FASTA for sequences [Default: %default]' ) parser.add_option( diff --git a/src/scripts/borzoi_sad_folds.py b/src/scripts/borzoi_sad_folds.py new file mode 100755 index 0000000..49f7959 --- /dev/null +++ b/src/scripts/borzoi_sad_folds.py @@ -0,0 +1,266 @@ +#!/usr/bin/env python +# Copyright 2019 Calico LLC + +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at + +# https://www.apache.org/licenses/LICENSE-2.0 + +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# ========================================================================= +from optparse import OptionParser, OptionGroup +import glob +import h5py +import json +import pdb +import os +import sys + +import numpy as np +import pandas as pd + +import slurm + +""" +borzoi_sad_folds.py + +Compute SAD scores across model folds. +""" + +################################################################################ +# main +################################################################################ +def main(): + usage = 'usage: %prog [options] ' + parser = OptionParser(usage) + + # sad + sad_options = OptionGroup(parser, 'borzoi_sad.py options') + sad_options.add_option( + '-f', + dest='genome_fasta', + default='%s/assembly/ucsc/hg38.fa' % os.environ.get('BORZOI_HG38', 'hg38'), + help='Genome FASTA for sequences [Default: %default]', + ) + sad_options.add_option( + '-o', + dest='out_dir', + default='sad', + help='Output directory for tables and plots [Default: %default]' + ) + sad_options.add_option( + '-p', + dest='processes', + default=None, + type='int', + help='Number of processes, passed by multi script' + ) + sad_options.add_option( + '--rc', + dest='rc', + default=False, + action='store_true', + help='Average forward and reverse complement predictions [Default: %default]' + ) + sad_options.add_option( + '--shifts', dest='shifts', + default='0', + type='str', + help='Ensemble prediction shifts [Default: %default]' + ) + sad_options.add_option( + '--stats', + dest='sad_stats', + default='SAD', + help='Comma-separated list of stats to save. [Default: %default]' + ) + sad_options.add_option( + '-t', + dest='targets_file', + default=None, + type='str', + help='File specifying target indexes and labels in table format' + ) + sad_options.add_option( + '-u', + dest='untransform_old', + default=False, + action='store_true', + ) + sad_options.add_option( + '--no_untransform', + dest='no_untransform', + default=False, + action='store_true', + ) + parser.add_option_group(sad_options) + + # cross-fold + fold_options = OptionGroup(parser, 'cross-fold options') + fold_options.add_option( + '-c', + dest='crosses', + default=1, + type='int', + help='Number of cross-fold rounds [Default:%default]', + ) + fold_options.add_option( + '--folds', + dest='fold_subset', + default=1, + type='int', + help='Run a subset of folds [Default:%default]', + ) + fold_options.add_option( + '--f_list', + dest='fold_subset_list', + default=None, + help='Run a subset of folds (encoded as comma-separated string) [Default:%default]', + ) + fold_options.add_option( + '-d', + dest='data_head', + default=None, + type='int', + help='Index for dataset/head [Default: %default]' + ) + fold_options.add_option( + '-e', + dest='conda_env', + default='tf210', + help='Anaconda environment [Default: %default]' + ) + fold_options.add_option( + '--name', + dest='name', + default='sad', + help='SLURM name prefix [Default: %default]' + ) + fold_options.add_option( + '--max_proc', + dest='max_proc', + default=None, + type='int', + help='Maximum concurrent processes [Default: %default]' + ) + fold_options.add_option( + '-q', + dest='queue', + default='geforce', + help='SLURM queue on which to run the jobs [Default: %default]' + ) + fold_options.add_option( + '-r', + dest='restart', + default=False, + action='store_true', + help='Restart a partially completed job [Default: %default]' + ) + fold_options.add_option( + '--vcf', + dest='vcf_file', + default='/home/jlinder/seqnn/data/satmutmpra/satmutmpra_v1.vcf' + ) + parser.add_option_group(fold_options) + + (options, args) = parser.parse_args() + + if len(args) != 2: + parser.error('Must provide parameters file and cross-fold directory') + else: + params_file = args[0] + exp_dir = args[1] + + ####################################################### + # prep work + + # set folds + num_folds = 1 + if options.fold_subset is not None: + num_folds = options.fold_subset + + fold_index = [fold_i for fold_i in range(num_folds)] + + # subset folds (list) + if options.fold_subset_list is not None: + fold_index = [int(fold_str) for fold_str in options.fold_subset_list.split(",")] + + ################################################################ + # SNP scores + + # command base + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += 'conda activate %s;' % options.conda_env + cmd_base += ' echo $HOSTNAME;' + + jobs = [] + + for ci in range(options.crosses): + for fi in fold_index: + it_dir = '%s/f%dc%d' % (exp_dir, fi, ci) + name = '%s-f%dc%d' % (options.name, fi, ci) + + # update output directory + it_out_dir = '%s/%s' % (it_dir, options.out_dir) + os.makedirs(it_out_dir, exist_ok=True) + + model_file = '%s/train/model_best.h5' % it_dir + if options.data_head is not None: + model_file = '%s/train/model%d_best.h5' % (it_dir, options.data_head) + + cmd_fold = '%s time borzoi_sad.py %s %s' % (cmd_base, params_file, model_file) + + # variant scoring job + job_out_dir = it_out_dir + if not options.restart or not os.path.isfile('%s/sad.h5'%job_out_dir): + cmd_job = '%s %s' % (cmd_fold, options.vcf_file) + cmd_job += ' %s' % options_string(options, sad_options, job_out_dir) + j = slurm.Job(cmd_job, '%s' % name, + '%s.out'%job_out_dir, '%s.err'%job_out_dir, '%s.sb'%job_out_dir, + queue=options.queue, gpu=1, + mem=45000, time='30-0:0:0') + jobs.append(j) + + slurm.multi_run(jobs, max_proc=options.max_proc, verbose=True, + launch_sleep=10, update_sleep=60) + +def options_string(options, group_options, rep_dir): + options_str = '' + + for opt in group_options.option_list: + opt_str = opt.get_opt_string() + opt_value = options.__dict__[opt.dest] + + # wrap askeriks in "" + if type(opt_value) == str and opt_value.find('*') != -1: + opt_value = '"%s"' % opt_value + + # no value for bools + elif type(opt_value) == bool: + if not opt_value: + opt_str = '' + opt_value = '' + + # skip Nones + elif opt_value is None: + opt_str = '' + opt_value = '' + + # modify + elif opt.dest == 'out_dir': + opt_value = rep_dir + + options_str += ' %s %s' % (opt_str, opt_value) + + return options_str + +################################################################################ +# __main__ +################################################################################ +if __name__ == '__main__': + main() diff --git a/src/scripts/borzoi_satg_gene.py b/src/scripts/borzoi_satg_gene.py index eb3c5c6..1c96712 100755 --- a/src/scripts/borzoi_satg_gene.py +++ b/src/scripts/borzoi_satg_gene.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -# Copyright 2022 Calico LLC +# Copyright 2017 Calico LLC # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -13,20 +13,23 @@ # See the License for the specific language governing permissions and # limitations under the License. # ========================================================================= +from __future__ import print_function + from optparse import OptionParser import gc import json import os -import pickle +import time import h5py import numpy as np import pandas as pd import pysam +import tensorflow as tf from baskerville.dataset import targets_prep_strand -from baskerville import dna_io +from baskerville import dna as dna_io from baskerville import gene as bgene from baskerville import seqnn @@ -38,14 +41,14 @@ ################################################################################ # main -################################################################################ +# ############################################################################### def main(): usage = "usage: %prog [options] " parser = OptionParser(usage) parser.add_option( - "-f", + "--fa", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( @@ -54,13 +57,6 @@ def main(): default="satg_out", help="Output directory [Default: %default]", ) - parser.add_option( - "-p", - dest="processes", - default=None, - type="int", - help="Number of processes, passed by multi script", - ) parser.add_option( "--rc", dest="rc", @@ -68,6 +64,27 @@ def main(): action="store_true", help="Ensemble forward and reverse complement predictions [Default: %default]", ) + parser.add_option( + "-f", + dest="folds", + default="0", + type="str", + help="Model folds to use in ensemble (comma-separated list) [Default: %default]", + ) + parser.add_option( + '-c', + dest='crosses', + default="0", + type="str", + help='Model crosses (replicates) to use in ensemble (comma-separated list) [Default:%default]', + ) + parser.add_option( + "--head", + dest="head_i", + default=0, + type="int", + help="Model head index [Default: %default]", + ) parser.add_option( "--shifts", dest="shifts", @@ -83,11 +100,67 @@ def main(): help="Aggregate entire gene span [Default: %default]", ) parser.add_option( - "--sum", - dest="sum_targets", + "--clip_soft", + dest="clip_soft", + default=None, + type="float", + help="Model clip_soft setting [Default: %default]", + ) + parser.add_option( + "--track_scale", + dest="track_scale", + default=0.02, + type="float", + help="Target transform scale [Default: %default]", + ) + parser.add_option( + "--track_transform", + dest="track_transform", + default=0.75, + type="float", + help="Target transform exponent [Default: %default]", + ) + parser.add_option( + "--untransform_old", + dest="untransform_old", + default=False, + action="store_true", + help="Run gradients with old version of inverse transforms [Default: %default]", + ) + parser.add_option( + "--no_untransform", + dest="no_untransform", + default=False, + action="store_true", + help="Run gradients with no inverse transforms [Default: %default]", + ) + parser.add_option( + "--get_preds", + dest="get_preds", default=False, action="store_true", - help="Sum targets for single output [Default: %default]", + help="Store scalar predictions in addition to their gradients [Default: %default]", + ) + parser.add_option( + "--pseudo_qtl", + dest="pseudo_qtl", + default=None, + type="float", + help="Quantile of predicted scalars to choose as pseudo count [Default: %default]", + ) + parser.add_option( + "--pseudo_tissue", + dest="pseudo_tissue", + default=None, + type="str", + help="Tissue to filter genes on when calculating pseudo count [Default: %default]", + ) + parser.add_option( + "--gene_file", + dest="gene_file", + default=None, + type="str", + help="Csv-file of gene metadata [Default: %default]", ) parser.add_option( "-t", @@ -101,43 +174,16 @@ def main(): if len(args) == 3: # single worker params_file = args[0] - model_file = args[1] + model_folder = args[1] genes_gtf_file = args[2] - - elif len(args) == 4: - # master script - options_pkl_file = args[0] - params_file = args[1] - model_file = args[2] - genes_gtf_file = args[3] - - # load options - options_pkl = open(options_pkl_file, "rb") - options = pickle.load(options_pkl) - options_pkl.close() - - elif len(args) == 5: - # multi worker - options_pkl_file = args[0] - params_file = args[1] - model_file = args[2] - genes_gtf_file = args[3] - worker_index = int(args[4]) - - # load options - options_pkl = open(options_pkl_file, "rb") - options = pickle.load(options_pkl) - options_pkl.close() - - # update output directory - options.out_dir = "%s/job%d" % (options.out_dir, worker_index) - else: - parser.error("Must provide parameter and model files and BED file") + parser.error("Must provide parameter file, model folder and GTF file") if not os.path.isdir(options.out_dir): - os.mkdir(options.out_dir) + os.makedirs(options.out_dir, exist_ok=True) + options.folds = [int(fold) for fold in options.folds.split(",")] + options.crosses = [int(cross) for cross in options.crosses.split(",")] options.shifts = [int(shift) for shift in options.shifts.split(",")] ################################################################# @@ -161,18 +207,34 @@ def main(): [orig_new_index[ti] for ti in targets_df.strand_pair] ) targets_strand_df = targets_prep_strand(targets_df) - num_targets = targets_strand_df.shape[0] - if options.sum_targets: - num_targets = 1 + num_targets = 1 + + # Load gene dataframe and select tissue + tissue_genes = None + if options.gene_file is not None and options.pseudo_tissue is not None: + gene_df = pd.read_csv(options.gene_file, sep="\t") + gene_df = ( + gene_df.query("tissue == '" + str(options.pseudo_tissue) + "'") + .copy() + .reset_index(drop=True) + ) + gene_df = gene_df.drop(columns=["Unnamed: 0"]) + + # Get list of gene for tissue + tissue_genes = gene_df["gene_base"].values.tolist() - # params strand_pair unnecessary because I'm not building ensemble in graph + print("len(tissue_genes) = " + str(len(tissue_genes))) ################################################################# - # setup model + # load first model fold to get parameters seqnn_model = seqnn.SeqNN(params_model) - seqnn_model.restore(model_file) - seqnn_model.build_slice(targets_df.index, options.sum_targets) + seqnn_model.restore( + model_folder + "/f" + str(options.folds[0]) + "c0/train/model" + str(options.head_i) + "_best.h5", + options.head_i + ) + seqnn_model.build_slice(targets_df.index, False) + # seqnn_model.build_ensemble(options.rc, options.shifts) model_stride = seqnn_model.model_strides[0] model_crop = seqnn_model.target_crops[0] @@ -189,15 +251,6 @@ def main(): gene_list = sorted(transcriptome.genes.keys()) num_genes = len(gene_list) - # filter for worker genes - if options.processes is not None: - # determine boundaries - worker_bounds = np.linspace(0, num_genes, options.processes + 1, dtype="int") - worker_start = worker_bounds[worker_index] - worker_end = worker_bounds[worker_index + 1] - gene_list = [gene_list[gi] for gi in range(worker_start, worker_end)] - num_genes = len(gene_list) - ################################################################# # setup output @@ -219,80 +272,369 @@ def main(): genes_start.append(gene_start) genes_end.append(gene_end) - # initialize HDF5 - scores_h5_file = "%s/scores.h5" % options.out_dir - if os.path.isfile(scores_h5_file): - os.remove(scores_h5_file) - scores_h5 = h5py.File(scores_h5_file, "w") - scores_h5.create_dataset("seqs", dtype="bool", shape=(num_genes, seq_len, 4)) - scores_h5.create_dataset( - "grads", dtype="float16", shape=(num_genes, seq_len, 4, num_targets) - ) - scores_h5.create_dataset("gene", data=np.array(gene_list, dtype="S")) - scores_h5.create_dataset("chr", data=np.array(genes_chr, dtype="S")) - scores_h5.create_dataset("start", data=np.array(genes_start)) - scores_h5.create_dataset("end", data=np.array(genes_end)) - scores_h5.create_dataset("strand", data=np.array(genes_strand, dtype="S")) - ################################################################# # predict scores, write output - for gi, gene_id in enumerate(gene_list): - print("Predicting %d, %s" % (gi, gene_id), flush=True) - gene = transcriptome.genes[gene_id] - - # make sequence - seq_1hot = make_seq_1hot( - genome_open, genes_chr[gi], genes_start[gi], genes_end[gi], seq_len - ) - - # determine output sequence start - seq_out_start = genes_start[gi] + model_stride * model_crop - seq_out_len = model_stride * target_length - - # determine output positions - gene_slice = gene.output_slice( - seq_out_start, seq_out_len, model_stride, options.span - ) - if options.rc: - gene_slice_rc = target_length - gene_slice - 1 - - if len(gene_slice) == 0: - print("WARNING: %s no gene positions found." % gene_id) - grads = np.zeros((seq_len, 4, num_targets), dtype="float16") + buffer_size = 1024 + + print("clip_soft = " + str(options.clip_soft)) + + print("n genes = " + str(len(genes_chr))) + + # loop over folds + for fold_ix in options.folds: + for cross_ix in options.crosses: + + print("-- fold = f" + str(fold_ix) + "c" + str(cross_ix) + " --") + + # (re-)initialize HDF5 + scores_h5_file = "%s/scores_f%dc%d.h5" % (options.out_dir, fold_ix, cross_ix) + if os.path.isfile(scores_h5_file): + os.remove(scores_h5_file) + scores_h5 = h5py.File(scores_h5_file, "w") + scores_h5.create_dataset("seqs", dtype="bool", shape=(num_genes, seq_len, 4)) + scores_h5.create_dataset( + "grads", dtype="float16", shape=(num_genes, seq_len, 4, num_targets) + ) + if options.get_preds: + scores_h5.create_dataset( + "preds", dtype="float32", shape=(num_genes, num_targets) + ) + scores_h5.create_dataset("gene", data=np.array(gene_list, dtype="S")) + scores_h5.create_dataset("chr", data=np.array(genes_chr, dtype="S")) + scores_h5.create_dataset("start", data=np.array(genes_start)) + scores_h5.create_dataset("end", data=np.array(genes_end)) + scores_h5.create_dataset("strand", data=np.array(genes_strand, dtype="S")) + + # load model fold + seqnn_model = seqnn.SeqNN(params_model) + seqnn_model.restore( + model_folder + "/f" + str(fold_ix) + "c" + str(cross_ix) + "/train/model" + str(options.head_i) + "_best.h5", + options.head_i + ) + seqnn_model.build_slice(targets_df.index, False) + + # optionally get (and store) scalar predictions before computing their gradients + if options.get_preds: + print(" - (prediction) - ", flush=True) + + for shift in options.shifts: + print("Processing shift %d" % shift, flush=True) + + for rev_comp in [False, True] if options.rc else [False]: + + if options.rc: + print( + "Fwd/rev = %s" % ("fwd" if not rev_comp else "rev"), + flush=True, + ) + + seq_1hots = [] + gene_slices = [] + gene_targets = [] + + for gi, gene_id in enumerate(gene_list): + + if gi % 500 == 0: + print("Processing %d, %s" % (gi, gene_id), flush=True) + + gene = transcriptome.genes[gene_id] + + # make sequence + seq_1hot = make_seq_1hot( + genome_open, + genes_chr[gi], + genes_start[gi], + genes_end[gi], + seq_len, + ) + seq_1hot = dna_io.hot1_augment(seq_1hot, shift=shift) + + # determine output sequence start + seq_out_start = genes_start[gi] + model_stride * model_crop + seq_out_len = model_stride * target_length + + # determine output positions + gene_slice = gene.output_slice( + seq_out_start, seq_out_len, model_stride, options.span + ) + + if rev_comp: + seq_1hot = dna_io.hot1_rc(seq_1hot) + gene_slice = target_length - gene_slice - 1 + + # slice relevant strand targets + if genes_strand[gi] == "+": + gene_strand_mask = ( + (targets_df.strand != "-") + if not rev_comp + else (targets_df.strand != "+") + ) + else: + gene_strand_mask = ( + (targets_df.strand != "+") + if not rev_comp + else (targets_df.strand != "-") + ) + + gene_target = np.array( + targets_df.index[gene_strand_mask].values + ) + + # accumulate data tensors + seq_1hots.append(seq_1hot[None, ...]) + gene_slices.append(gene_slice[None, ...]) + gene_targets.append(gene_target[None, ...]) + + if gi == len(gene_list) - 1 or len(seq_1hots) >= buffer_size: + + # concat sequences + seq_1hots = np.concatenate(seq_1hots, axis=0) + + # pad gene slices to same length (mark valid positions in mask tensor) + max_slice_len = int( + np.max( + [gene_slice.shape[1] for gene_slice in gene_slices] + ) + ) + + gene_masks = np.zeros( + (len(gene_slices), max_slice_len), dtype="float32" + ) + gene_slices_padded = np.zeros( + (len(gene_slices), max_slice_len), dtype="int32" + ) + for gii, gene_slice in enumerate(gene_slices): + for j in range(gene_slice.shape[1]): + gene_masks[gii, j] = 1.0 + gene_slices_padded[gii, j] = gene_slice[0, j] + + gene_slices = gene_slices_padded + + # concat gene-specific targets + gene_targets = np.concatenate(gene_targets, axis=0) + + # batch call count predictions + preds = predict_counts( + seqnn_model, + seq_1hots, + head_i=0, + target_slice=gene_targets, + pos_slice=gene_slices, + pos_mask=gene_masks, + chunk_size=buffer_size, + batch_size=1, + track_scale=options.track_scale, + track_transform=options.track_transform, + clip_soft=options.clip_soft, + untransform_old=options.untransform_old, + use_mean=False, + dtype="float32", + ) + + # save predictions + for gii, gene_slice in enumerate(gene_slices): + h5_gi = (gi // buffer_size) * buffer_size + gii + + # write to HDF5 + scores_h5["preds"][h5_gi, :] += preds[gii] / float( + len(options.shifts) + ) + + # clear sequence buffer + seq_1hots = [] + gene_slices = [] + gene_targets = [] + + # collect garbage + gc.collect() + + # optionally set pseudo count from predictions + pseudo_count = 0.0 + if options.pseudo_qtl is not None: + gene_preds = scores_h5["preds"][:] + + # filter on tissue + tissue_preds = None + + if tissue_genes is not None: + tissue_set = set(tissue_genes) + + # get subset of genes and predictions belonging to the pseudo count tissue + tissue_preds = [] + for gi, gene_id in enumerate(gene_list): + if gene_id.split(".")[0] in tissue_set: + tissue_preds.append(gene_preds[gi, 0]) + + tissue_preds = np.array(tissue_preds, dtype="float32") + else: + tissue_preds = np.array(gene_preds[:, 0], dtype="float32") + + print("tissue_preds.shape[0] = " + str(tissue_preds.shape[0])) + + print("np.min(tissue_preds) = " + str(np.min(tissue_preds))) + print("np.max(tissue_preds) = " + str(np.max(tissue_preds))) + + # set pseudo count based on quantile of predictions + pseudo_count = np.quantile(tissue_preds, q=options.pseudo_qtl) + + print("") + print("pseudo_count = " + str(round(pseudo_count, 6))) + + # compute gradients + print(" - (gradients) - ", flush=True) - else: - grads_ens = [] for shift in options.shifts: - seq_1hot_aug = dna_io.hot1_augment(seq_1hot, shift=shift) - grads_aug = seqnn_model.gradients(seq_1hot_aug, pos_slice=gene_slice) - grads_aug = unaugment_grads(grads_aug, fwdrc=True, shift=shift) - grads_ens.append(grads_aug) - - if options.rc: - seq_1hot_aug = dna_io.hot1_rc(seq_1hot_aug) - grads_aug = seqnn_model.gradients( - seq_1hot_aug, pos_slice=gene_slice_rc - ) - grads_aug = unaugment_grads(grads_aug, fwdrc=False, shift=shift) - grads_aug = grads_aug[..., targets_strand_pair] - grads_ens.append(grads_aug) - - # ensemble mean - grads = np.array(grads_ens).mean(axis=0) - - # slice relevant strand targets - if genes_strand[gi] == "+": - gene_strand_mask = targets_df.strand != "-" - else: - gene_strand_mask = targets_df.strand != "+" - grads = grads[..., gene_strand_mask] - - # write to HDF5 - scores_h5["seqs"][gi] = seq_1hot - scores_h5["grads"][gi] = grads - - gc.collect() + print("Processing shift %d" % shift, flush=True) + + for rev_comp in [False, True] if options.rc else [False]: + + if options.rc: + print( + "Fwd/rev = %s" % ("fwd" if not rev_comp else "rev"), flush=True + ) + + seq_1hots = [] + gene_slices = [] + gene_targets = [] + + for gi, gene_id in enumerate(gene_list): + + if gi % 500 == 0: + print("Processing %d, %s" % (gi, gene_id), flush=True) + + gene = transcriptome.genes[gene_id] + + # make sequence + seq_1hot = make_seq_1hot( + genome_open, + genes_chr[gi], + genes_start[gi], + genes_end[gi], + seq_len, + ) + seq_1hot = dna_io.hot1_augment(seq_1hot, shift=shift) + + # determine output sequence start + seq_out_start = genes_start[gi] + model_stride * model_crop + seq_out_len = model_stride * target_length + + # determine output positions + gene_slice = gene.output_slice( + seq_out_start, seq_out_len, model_stride, options.span + ) + + if rev_comp: + seq_1hot = dna_io.hot1_rc(seq_1hot) + gene_slice = target_length - gene_slice - 1 + + # slice relevant strand targets + if genes_strand[gi] == "+": + gene_strand_mask = ( + (targets_df.strand != "-") + if not rev_comp + else (targets_df.strand != "+") + ) + else: + gene_strand_mask = ( + (targets_df.strand != "+") + if not rev_comp + else (targets_df.strand != "-") + ) + + gene_target = np.array(targets_df.index[gene_strand_mask].values) + + # accumulate data tensors + seq_1hots.append(seq_1hot[None, ...]) + gene_slices.append(gene_slice[None, ...]) + gene_targets.append(gene_target[None, ...]) + + if gi == len(gene_list) - 1 or len(seq_1hots) >= buffer_size: + + # concat sequences + seq_1hots = np.concatenate(seq_1hots, axis=0) + + # pad gene slices to same length (mark valid positions in mask tensor) + max_slice_len = int( + np.max([gene_slice.shape[1] for gene_slice in gene_slices]) + ) + + gene_masks = np.zeros( + (len(gene_slices), max_slice_len), dtype="float32" + ) + gene_slices_padded = np.zeros( + (len(gene_slices), max_slice_len), dtype="int32" + ) + for gii, gene_slice in enumerate(gene_slices): + for j in range(gene_slice.shape[1]): + gene_masks[gii, j] = 1.0 + gene_slices_padded[gii, j] = gene_slice[0, j] + + gene_slices = gene_slices_padded + + # concat gene-specific targets + gene_targets = np.concatenate(gene_targets, axis=0) + + # batch call gradient computation + grads = seqnn_model.gradients( + seq_1hots, + head_i=0, + target_slice=gene_targets, + pos_slice=gene_slices, + pos_mask=gene_masks, + chunk_size=buffer_size, + batch_size=1, + track_scale=options.track_scale, + track_transform=options.track_transform, + clip_soft=options.clip_soft, + pseudo_count=pseudo_count, + untransform_old=options.untransform_old, + no_untransform=options.no_untransform, + use_mean=False, + use_ratio=False, + use_logodds=False, + subtract_avg=True, + input_gate=False, + dtype="float16", + ) + + # undo augmentations and save gradients + for gii, gene_slice in enumerate(gene_slices): + grad = unaugment_grads( + grads[gii, :, :, None], + fwdrc=(not rev_comp), + shift=shift, + ) + + h5_gi = (gi // buffer_size) * buffer_size + gii + + # write to HDF5 + scores_h5["grads"][h5_gi] += grad + + # clear sequence buffer + seq_1hots = [] + gene_slices = [] + gene_targets = [] + + # collect garbage + gc.collect() + + # save sequences and normalize gradients by total size of ensemble + for gi, gene_id in enumerate(gene_list): + + # re-make original sequence + seq_1hot = make_seq_1hot( + genome_open, genes_chr[gi], genes_start[gi], genes_end[gi], seq_len + ) + + # write to HDF5 + scores_h5["seqs"][gi] = seq_1hot + scores_h5["grads"][gi] /= float( + (len(options.shifts) * (2 if options.rc else 1)) + ) + + # collect garbage + gc.collect() # close files genome_open.close() @@ -344,8 +686,219 @@ def make_seq_1hot(genome_open, chrm, start, end, seq_len): return seq_1hot +# tf code for predicting raw sum-of-expression counts on GPU +@tf.function +def _count_func( + model, + seq_1hot, + target_slice, + pos_slice, + pos_mask=None, + track_scale=1.0, + track_transform=1.0, + clip_soft=None, + untransform_old=False, + use_mean=False, +): + + # predict + preds = tf.gather( + model(seq_1hot, training=False), target_slice, axis=-1, batch_dims=1 + ) + + if untransform_old: + # undo scale + preds = preds / track_scale + + # undo clip_soft + if clip_soft is not None: + preds = tf.where( + preds > clip_soft, (preds - clip_soft) ** 2 + clip_soft, preds + ) + + # undo sqrt + preds = preds ** (1. / track_transform) + else: + # undo clip_soft + if clip_soft is not None: + preds = tf.where( + preds > clip_soft, (preds - clip_soft + 1) ** 2 + clip_soft - 1, preds + ) + + # undo sqrt + preds = -1 + (preds + 1) ** (1. / track_transform) + + # scale + preds = preds / track_scale + + # aggregate over tracks (average) + preds = tf.reduce_mean(preds, axis=-1) + + # slice specified positions + preds_slice = tf.gather(preds, pos_slice, axis=-1, batch_dims=1) + if pos_mask is not None: + preds_slice = preds_slice * pos_mask + + # aggregate over positions + if not use_mean: + preds_agg = tf.reduce_sum(preds_slice, axis=-1) + else: + if pos_mask is not None: + preds_agg = tf.reduce_sum(preds_slice, axis=-1) / tf.reduce_sum( + pos_mask, axis=-1 + ) + else: + preds_agg = tf.reduce_mean(preds_slice, axis=-1) + + return preds_agg + + +# code for getting model predictions from a tensor of input sequence patterns +def predict_counts( + seqnn_model, + seq_1hot, + head_i=None, + target_slice=None, + pos_slice=None, + pos_mask=None, + chunk_size=None, + batch_size=1, + track_scale=1.0, + track_transform=1.0, + clip_soft=None, + untransform_old=False, + use_mean=False, + dtype="float32", +): + + # start time + t0 = time.time() + + # choose model + if seqnn_model.ensemble is not None: + model = seqnn_model.ensemble + elif head_i is not None: + model = seqnn_model.models[head_i] + else: + model = seqnn_model.model + + # verify tensor shape(s) + seq_1hot = seq_1hot.astype("float32") + target_slice = np.array(target_slice).astype("int32") + pos_slice = np.array(pos_slice).astype("int32") + + # convert constants to tf tensors + track_scale = tf.constant(track_scale, dtype=tf.float32) + track_transform = tf.constant(track_transform, dtype=tf.float32) + if clip_soft is not None: + clip_soft = tf.constant(clip_soft, dtype=tf.float32) + + if pos_mask is not None: + pos_mask = np.array(pos_mask).astype("float32") + + if len(seq_1hot.shape) < 3: + seq_1hot = seq_1hot[None, ...] + + if len(target_slice.shape) < 2: + target_slice = target_slice[None, ...] + + if len(pos_slice.shape) < 2: + pos_slice = pos_slice[None, ...] + + if pos_mask is not None and len(pos_mask.shape) < 2: + pos_mask = pos_mask[None, ...] + + # chunk parameters + num_chunks = 1 + if chunk_size is None: + chunk_size = seq_1hot.shape[0] + else: + num_chunks = int(np.ceil(seq_1hot.shape[0] / chunk_size)) + + # loop over chunks + pred_chunks = [] + for ci in range(num_chunks): + + # collect chunk + seq_1hot_chunk = seq_1hot[ci * chunk_size : (ci + 1) * chunk_size, ...] + target_slice_chunk = target_slice[ci * chunk_size : (ci + 1) * chunk_size, ...] + pos_slice_chunk = pos_slice[ci * chunk_size : (ci + 1) * chunk_size, ...] + + pos_mask_chunk = None + if pos_mask is not None: + pos_mask_chunk = pos_mask[ci * chunk_size : (ci + 1) * chunk_size, ...] + + actual_chunk_size = seq_1hot_chunk.shape[0] + + # convert to tf tensors + seq_1hot_chunk = tf.convert_to_tensor(seq_1hot_chunk, dtype=tf.float32) + target_slice_chunk = tf.convert_to_tensor(target_slice_chunk, dtype=tf.int32) + pos_slice_chunk = tf.convert_to_tensor(pos_slice_chunk, dtype=tf.int32) + + if pos_mask is not None: + pos_mask_chunk = tf.convert_to_tensor(pos_mask_chunk, dtype=tf.float32) + + # batching parameters + num_batches = int(np.ceil(actual_chunk_size / batch_size)) + + # loop over batches + pred_batches = [] + for bi in range(num_batches): + + # collect batch + seq_1hot_batch = seq_1hot_chunk[ + bi * batch_size : (bi + 1) * batch_size, ... + ] + target_slice_batch = target_slice_chunk[ + bi * batch_size : (bi + 1) * batch_size, ... + ] + pos_slice_batch = pos_slice_chunk[ + bi * batch_size : (bi + 1) * batch_size, ... + ] + + pos_mask_batch = None + if pos_mask is not None: + pos_mask_batch = pos_mask_chunk[ + bi * batch_size : (bi + 1) * batch_size, ... + ] + + pred_batch = ( + _count_func( + model, + seq_1hot_batch, + target_slice_batch, + pos_slice_batch, + pos_mask_batch, + track_scale, + track_transform, + clip_soft, + untransform_old, + use_mean, + ) + .numpy() + .astype(dtype) + ) + + pred_batches.append(pred_batch) + + # concat predicted batches + preds = np.concatenate(pred_batches, axis=0) + + pred_chunks.append(preds) + + # collect garbage + gc.collect() + + # concat predicted chunks + preds = np.concatenate(pred_chunks, axis=0) + + print("Made predictions in %ds" % (time.time() - t0)) + + return preds + + ################################################################################ # __main__ -################################################################################ +# ############################################################################### if __name__ == "__main__": main() diff --git a/src/scripts/borzoi_satg_gene_gpu_crispr_ism_shuffle.py b/src/scripts/borzoi_satg_gene_crispr_ism_shuffle.py old mode 100644 new mode 100755 similarity index 98% rename from src/scripts/borzoi_satg_gene_gpu_crispr_ism_shuffle.py rename to src/scripts/borzoi_satg_gene_crispr_ism_shuffle.py index 6177ef0..b3fd477 --- a/src/scripts/borzoi_satg_gene_gpu_crispr_ism_shuffle.py +++ b/src/scripts/borzoi_satg_gene_crispr_ism_shuffle.py @@ -35,7 +35,7 @@ import pygene import tensorflow as tf -from baskerville import dna_io +from baskerville import dna as dna_io from baskerville import gene as bgene from baskerville import seqnn from baskerville.dataset import targets_prep_strand @@ -43,7 +43,7 @@ from scipy.ndimage import gaussian_filter1d ''' -borzoi_satg_gene_gpu_crispr_ism_shuffle.py +borzoi_satg_gene_crispr_ism_shuffle.py Perform a windowed shuffle analysis for genes specified in a GTF file, targeting regions specified in a separate csv. ''' @@ -58,7 +58,7 @@ def main(): parser.add_option( "--fa", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( @@ -84,9 +84,9 @@ def main(): parser.add_option( '-c', dest='crosses', - default=1, - type='int', - help='Number of cross-fold rounds [Default:%default]', + default="0", + type="str", + help='Model crosses (replicates) to use in ensemble (comma-separated list) [Default:%default]', ) parser.add_option( "--head", @@ -218,9 +218,10 @@ def main(): parser.error('Must provide parameter file, model folder and BED file') if not os.path.isdir(options.out_dir): - os.mkdir(options.out_dir) + os.makedirs(options.out_dir, exist_ok=True) options.folds = [int(fold) for fold in options.folds.split(',')] + options.crosses = [int(cross) for cross in options.crosses.split(",")] options.shifts = [int(shift) for shift in options.shifts.split(',')] ################################################################# diff --git a/src/scripts/borzoi_satg_gene_gpu_focused_ism.py b/src/scripts/borzoi_satg_gene_focused_ism.py similarity index 98% rename from src/scripts/borzoi_satg_gene_gpu_focused_ism.py rename to src/scripts/borzoi_satg_gene_focused_ism.py index 0f6cd08..f095be8 100755 --- a/src/scripts/borzoi_satg_gene_gpu_focused_ism.py +++ b/src/scripts/borzoi_satg_gene_focused_ism.py @@ -27,12 +27,12 @@ import tensorflow as tf from baskerville.dataset import targets_prep_strand -from baskerville import dna_io +from baskerville import dna as dna_io from baskerville import gene as bgene from baskerville import seqnn """ -borzoi_satg_gene_gpu_focused_ism.py +borzoi_satg_gene_focused_ism.py Perform an ISM analysis for genes specified in a GTF file, targeting high-saliency regions based on gradient scores. """ @@ -46,7 +46,7 @@ def main(): parser.add_option( "--fa", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( @@ -72,9 +72,9 @@ def main(): parser.add_option( '-c', dest='crosses', - default=1, - type='int', - help='Number of cross-fold rounds [Default:%default]', + default="0", + type="str", + help='Model crosses (replicates) to use in ensemble (comma-separated list) [Default:%default]', ) parser.add_option( "--head", @@ -228,9 +228,10 @@ def main(): parser.error("Must provide parameter file, model folder and GTF file") if not os.path.isdir(options.out_dir): - os.mkdir(options.out_dir) + os.makedirs(options.out_dir, exist_ok=True) options.folds = [int(fold) for fold in options.folds.split(",")] + options.crosses = [int(cross) for cross in options.crosses.split(",")] options.shifts = [int(shift) for shift in options.shifts.split(",")] options.tissue_files = [tissue for tissue in options.tissue_files.split(",")] diff --git a/src/scripts/borzoi_satg_gene_gpu.py b/src/scripts/borzoi_satg_gene_gpu.py deleted file mode 100755 index fd22b45..0000000 --- a/src/scripts/borzoi_satg_gene_gpu.py +++ /dev/null @@ -1,903 +0,0 @@ -#!/usr/bin/env python -# Copyright 2017 Calico LLC -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# https://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ========================================================================= -from __future__ import print_function - -from optparse import OptionParser - -import gc -import json -import os -import time - -import h5py -import numpy as np -import pandas as pd -import pysam -import tensorflow as tf - -from baskerville.dataset import targets_prep_strand -from baskerville import dna_io -from baskerville import gene as bgene -from baskerville import seqnn - -""" -borzoi_satg_gene_gpu.py - -Perform a gradient saliency analysis for genes specified in a GTF file (GPU-friendly). -""" - -################################################################################ -# main -# ############################################################################### -def main(): - usage = "usage: %prog [options] " - parser = OptionParser(usage) - parser.add_option( - "--fa", - dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], - help="Genome FASTA for sequences [Default: %default]", - ) - parser.add_option( - "-o", - dest="out_dir", - default="satg_out", - help="Output directory [Default: %default]", - ) - parser.add_option( - "--rc", - dest="rc", - default=False, - action="store_true", - help="Ensemble forward and reverse complement predictions [Default: %default]", - ) - parser.add_option( - "-f", - dest="folds", - default="0", - type="str", - help="Model folds to use in ensemble (comma-separated list) [Default: %default]", - ) - parser.add_option( - '-c', - dest='crosses', - default=1, - type='int', - help='Number of cross-fold rounds [Default:%default]', - ) - parser.add_option( - "--head", - dest="head_i", - default=0, - type="int", - help="Model head index [Default: %default]", - ) - parser.add_option( - "--shifts", - dest="shifts", - default="0", - type="str", - help="Ensemble prediction shifts [Default: %default]", - ) - parser.add_option( - "--span", - dest="span", - default=False, - action="store_true", - help="Aggregate entire gene span [Default: %default]", - ) - parser.add_option( - "--clip_soft", - dest="clip_soft", - default=None, - type="float", - help="Model clip_soft setting [Default: %default]", - ) - parser.add_option( - "--track_scale", - dest="track_scale", - default=0.02, - type="float", - help="Target transform scale [Default: %default]", - ) - parser.add_option( - "--track_transform", - dest="track_transform", - default=0.75, - type="float", - help="Target transform exponent [Default: %default]", - ) - parser.add_option( - "--untransform_old", - dest="untransform_old", - default=False, - action="store_true", - help="Run gradients with old version of inverse transforms [Default: %default]", - ) - parser.add_option( - "--no_untransform", - dest="no_untransform", - default=False, - action="store_true", - help="Run gradients with no inverse transforms [Default: %default]", - ) - parser.add_option( - "--get_preds", - dest="get_preds", - default=False, - action="store_true", - help="Store scalar predictions in addition to their gradients [Default: %default]", - ) - parser.add_option( - "--pseudo_qtl", - dest="pseudo_qtl", - default=None, - type="float", - help="Quantile of predicted scalars to choose as pseudo count [Default: %default]", - ) - parser.add_option( - "--pseudo_tissue", - dest="pseudo_tissue", - default=None, - type="str", - help="Tissue to filter genes on when calculating pseudo count [Default: %default]", - ) - parser.add_option( - "--gene_file", - dest="gene_file", - default=None, - type="str", - help="Csv-file of gene metadata [Default: %default]", - ) - parser.add_option( - "-t", - dest="targets_file", - default=None, - type="str", - help="File specifying target indexes and labels in table format", - ) - (options, args) = parser.parse_args() - - if len(args) == 3: - # single worker - params_file = args[0] - model_folder = args[1] - genes_gtf_file = args[2] - else: - parser.error("Must provide parameter file, model folder and GTF file") - - if not os.path.isdir(options.out_dir): - os.mkdir(options.out_dir) - - options.folds = [int(fold) for fold in options.folds.split(",")] - options.shifts = [int(shift) for shift in options.shifts.split(",")] - - ################################################################# - # read parameters and targets - - # read model parameters - with open(params_file) as params_open: - params = json.load(params_open) - params_model = params["model"] - params_train = params["train"] - seq_len = params_model["seq_length"] - - if options.targets_file is None: - parser.error("Must provide targets table to properly handle strands.") - else: - targets_df = pd.read_csv(options.targets_file, sep="\t", index_col=0) - - # prep strand - orig_new_index = dict(zip(targets_df.index, np.arange(targets_df.shape[0]))) - targets_strand_pair = np.array( - [orig_new_index[ti] for ti in targets_df.strand_pair] - ) - targets_strand_df = targets_prep_strand(targets_df) - num_targets = 1 - - # Load gene dataframe and select tissue - tissue_genes = None - if options.gene_file is not None and options.pseudo_tissue is not None: - gene_df = pd.read_csv(options.gene_file, sep="\t") - gene_df = ( - gene_df.query("tissue == '" + str(options.pseudo_tissue) + "'") - .copy() - .reset_index(drop=True) - ) - gene_df = gene_df.drop(columns=["Unnamed: 0"]) - - # Get list of gene for tissue - tissue_genes = gene_df["gene_base"].values.tolist() - - print("len(tissue_genes) = " + str(len(tissue_genes))) - - ################################################################# - # load first model fold to get parameters - - seqnn_model = seqnn.SeqNN(params_model) - seqnn_model.restore( - model_folder + "/f" + str(options.folds[0]) + "c0/train/model" + str(options.head_i) + "_best.h5", - options.head_i - ) - seqnn_model.build_slice(targets_df.index, False) - # seqnn_model.build_ensemble(options.rc, options.shifts) - - model_stride = seqnn_model.model_strides[0] - model_crop = seqnn_model.target_crops[0] - target_length = seqnn_model.target_lengths[0] - - ################################################################# - # read genes - - # parse GTF - transcriptome = bgene.Transcriptome(genes_gtf_file) - - # order valid genes - genome_open = pysam.Fastafile(options.genome_fasta) - gene_list = sorted(transcriptome.genes.keys()) - num_genes = len(gene_list) - - ################################################################# - # setup output - - min_start = -model_stride * model_crop - - # choose gene sequences - genes_chr = [] - genes_start = [] - genes_end = [] - genes_strand = [] - for gene_id in gene_list: - gene = transcriptome.genes[gene_id] - genes_chr.append(gene.chrom) - genes_strand.append(gene.strand) - - gene_midpoint = gene.midpoint() - gene_start = max(min_start, gene_midpoint - seq_len // 2) - gene_end = gene_start + seq_len - genes_start.append(gene_start) - genes_end.append(gene_end) - - ################################################################# - # predict scores, write output - - buffer_size = 1024 - - print("clip_soft = " + str(options.clip_soft)) - - print("n genes = " + str(len(genes_chr))) - - # loop over folds - for fold_ix in options.folds: - for cross_ix in options.crosses: - - print("-- fold = f" + str(fold_ix) + "c" + str(cross_ix) + " --") - - # (re-)initialize HDF5 - scores_h5_file = "%s/scores_f%dc%d.h5" % (options.out_dir, fold_ix, cross_ix) - if os.path.isfile(scores_h5_file): - os.remove(scores_h5_file) - scores_h5 = h5py.File(scores_h5_file, "w") - scores_h5.create_dataset("seqs", dtype="bool", shape=(num_genes, seq_len, 4)) - scores_h5.create_dataset( - "grads", dtype="float16", shape=(num_genes, seq_len, 4, num_targets) - ) - if options.get_preds: - scores_h5.create_dataset( - "preds", dtype="float32", shape=(num_genes, num_targets) - ) - scores_h5.create_dataset("gene", data=np.array(gene_list, dtype="S")) - scores_h5.create_dataset("chr", data=np.array(genes_chr, dtype="S")) - scores_h5.create_dataset("start", data=np.array(genes_start)) - scores_h5.create_dataset("end", data=np.array(genes_end)) - scores_h5.create_dataset("strand", data=np.array(genes_strand, dtype="S")) - - # load model fold - seqnn_model = seqnn.SeqNN(params_model) - seqnn_model.restore( - model_folder + "/f" + str(fold_ix) + "c" + str(cross_ix) + "/train/model" + str(options.head_i) + "_best.h5", - options.head_i - ) - seqnn_model.build_slice(targets_df.index, False) - - # optionally get (and store) scalar predictions before computing their gradients - if options.get_preds: - print(" - (prediction) - ", flush=True) - - for shift in options.shifts: - print("Processing shift %d" % shift, flush=True) - - for rev_comp in [False, True] if options.rc else [False]: - - if options.rc: - print( - "Fwd/rev = %s" % ("fwd" if not rev_comp else "rev"), - flush=True, - ) - - seq_1hots = [] - gene_slices = [] - gene_targets = [] - - for gi, gene_id in enumerate(gene_list): - - if gi % 500 == 0: - print("Processing %d, %s" % (gi, gene_id), flush=True) - - gene = transcriptome.genes[gene_id] - - # make sequence - seq_1hot = make_seq_1hot( - genome_open, - genes_chr[gi], - genes_start[gi], - genes_end[gi], - seq_len, - ) - seq_1hot = dna_io.hot1_augment(seq_1hot, shift=shift) - - # determine output sequence start - seq_out_start = genes_start[gi] + model_stride * model_crop - seq_out_len = model_stride * target_length - - # determine output positions - gene_slice = gene.output_slice( - seq_out_start, seq_out_len, model_stride, options.span - ) - - if rev_comp: - seq_1hot = dna_io.hot1_rc(seq_1hot) - gene_slice = target_length - gene_slice - 1 - - # slice relevant strand targets - if genes_strand[gi] == "+": - gene_strand_mask = ( - (targets_df.strand != "-") - if not rev_comp - else (targets_df.strand != "+") - ) - else: - gene_strand_mask = ( - (targets_df.strand != "+") - if not rev_comp - else (targets_df.strand != "-") - ) - - gene_target = np.array( - targets_df.index[gene_strand_mask].values - ) - - # accumulate data tensors - seq_1hots.append(seq_1hot[None, ...]) - gene_slices.append(gene_slice[None, ...]) - gene_targets.append(gene_target[None, ...]) - - if gi == len(gene_list) - 1 or len(seq_1hots) >= buffer_size: - - # concat sequences - seq_1hots = np.concatenate(seq_1hots, axis=0) - - # pad gene slices to same length (mark valid positions in mask tensor) - max_slice_len = int( - np.max( - [gene_slice.shape[1] for gene_slice in gene_slices] - ) - ) - - gene_masks = np.zeros( - (len(gene_slices), max_slice_len), dtype="float32" - ) - gene_slices_padded = np.zeros( - (len(gene_slices), max_slice_len), dtype="int32" - ) - for gii, gene_slice in enumerate(gene_slices): - for j in range(gene_slice.shape[1]): - gene_masks[gii, j] = 1.0 - gene_slices_padded[gii, j] = gene_slice[0, j] - - gene_slices = gene_slices_padded - - # concat gene-specific targets - gene_targets = np.concatenate(gene_targets, axis=0) - - # batch call count predictions - preds = predict_counts( - seqnn_model, - seq_1hots, - head_i=0, - target_slice=gene_targets, - pos_slice=gene_slices, - pos_mask=gene_masks, - chunk_size=buffer_size, - batch_size=1, - track_scale=options.track_scale, - track_transform=options.track_transform, - clip_soft=options.clip_soft, - untransform_old=options.untransform_old, - use_mean=False, - dtype="float32", - ) - - # save predictions - for gii, gene_slice in enumerate(gene_slices): - h5_gi = (gi // buffer_size) * buffer_size + gii - - # write to HDF5 - scores_h5["preds"][h5_gi, :] += preds[gii] / float( - len(options.shifts) - ) - - # clear sequence buffer - seq_1hots = [] - gene_slices = [] - gene_targets = [] - - # collect garbage - gc.collect() - - # optionally set pseudo count from predictions - pseudo_count = 0.0 - if options.pseudo_qtl is not None: - gene_preds = scores_h5["preds"][:] - - # filter on tissue - tissue_preds = None - - if tissue_genes is not None: - tissue_set = set(tissue_genes) - - # get subset of genes and predictions belonging to the pseudo count tissue - tissue_preds = [] - for gi, gene_id in enumerate(gene_list): - if gene_id.split(".")[0] in tissue_set: - tissue_preds.append(gene_preds[gi, 0]) - - tissue_preds = np.array(tissue_preds, dtype="float32") - else: - tissue_preds = np.array(gene_preds[:, 0], dtype="float32") - - print("tissue_preds.shape[0] = " + str(tissue_preds.shape[0])) - - print("np.min(tissue_preds) = " + str(np.min(tissue_preds))) - print("np.max(tissue_preds) = " + str(np.max(tissue_preds))) - - # set pseudo count based on quantile of predictions - pseudo_count = np.quantile(tissue_preds, q=options.pseudo_qtl) - - print("") - print("pseudo_count = " + str(round(pseudo_count, 6))) - - # compute gradients - print(" - (gradients) - ", flush=True) - - for shift in options.shifts: - print("Processing shift %d" % shift, flush=True) - - for rev_comp in [False, True] if options.rc else [False]: - - if options.rc: - print( - "Fwd/rev = %s" % ("fwd" if not rev_comp else "rev"), flush=True - ) - - seq_1hots = [] - gene_slices = [] - gene_targets = [] - - for gi, gene_id in enumerate(gene_list): - - if gi % 500 == 0: - print("Processing %d, %s" % (gi, gene_id), flush=True) - - gene = transcriptome.genes[gene_id] - - # make sequence - seq_1hot = make_seq_1hot( - genome_open, - genes_chr[gi], - genes_start[gi], - genes_end[gi], - seq_len, - ) - seq_1hot = dna_io.hot1_augment(seq_1hot, shift=shift) - - # determine output sequence start - seq_out_start = genes_start[gi] + model_stride * model_crop - seq_out_len = model_stride * target_length - - # determine output positions - gene_slice = gene.output_slice( - seq_out_start, seq_out_len, model_stride, options.span - ) - - if rev_comp: - seq_1hot = dna_io.hot1_rc(seq_1hot) - gene_slice = target_length - gene_slice - 1 - - # slice relevant strand targets - if genes_strand[gi] == "+": - gene_strand_mask = ( - (targets_df.strand != "-") - if not rev_comp - else (targets_df.strand != "+") - ) - else: - gene_strand_mask = ( - (targets_df.strand != "+") - if not rev_comp - else (targets_df.strand != "-") - ) - - gene_target = np.array(targets_df.index[gene_strand_mask].values) - - # accumulate data tensors - seq_1hots.append(seq_1hot[None, ...]) - gene_slices.append(gene_slice[None, ...]) - gene_targets.append(gene_target[None, ...]) - - if gi == len(gene_list) - 1 or len(seq_1hots) >= buffer_size: - - # concat sequences - seq_1hots = np.concatenate(seq_1hots, axis=0) - - # pad gene slices to same length (mark valid positions in mask tensor) - max_slice_len = int( - np.max([gene_slice.shape[1] for gene_slice in gene_slices]) - ) - - gene_masks = np.zeros( - (len(gene_slices), max_slice_len), dtype="float32" - ) - gene_slices_padded = np.zeros( - (len(gene_slices), max_slice_len), dtype="int32" - ) - for gii, gene_slice in enumerate(gene_slices): - for j in range(gene_slice.shape[1]): - gene_masks[gii, j] = 1.0 - gene_slices_padded[gii, j] = gene_slice[0, j] - - gene_slices = gene_slices_padded - - # concat gene-specific targets - gene_targets = np.concatenate(gene_targets, axis=0) - - # batch call gradient computation - grads = seqnn_model.gradients( - seq_1hots, - head_i=0, - target_slice=gene_targets, - pos_slice=gene_slices, - pos_mask=gene_masks, - chunk_size=buffer_size, - batch_size=1, - track_scale=options.track_scale, - track_transform=options.track_transform, - clip_soft=options.clip_soft, - pseudo_count=pseudo_count, - untransform_old=options.untransform_old, - no_untransform=options.no_untransform, - use_mean=False, - use_ratio=False, - use_logodds=False, - subtract_avg=True, - input_gate=False, - dtype="float16", - ) - - # undo augmentations and save gradients - for gii, gene_slice in enumerate(gene_slices): - grad = unaugment_grads( - grads[gii, :, :, None], - fwdrc=(not rev_comp), - shift=shift, - ) - - h5_gi = (gi // buffer_size) * buffer_size + gii - - # write to HDF5 - scores_h5["grads"][h5_gi] += grad - - # clear sequence buffer - seq_1hots = [] - gene_slices = [] - gene_targets = [] - - # collect garbage - gc.collect() - - # save sequences and normalize gradients by total size of ensemble - for gi, gene_id in enumerate(gene_list): - - # re-make original sequence - seq_1hot = make_seq_1hot( - genome_open, genes_chr[gi], genes_start[gi], genes_end[gi], seq_len - ) - - # write to HDF5 - scores_h5["seqs"][gi] = seq_1hot - scores_h5["grads"][gi] /= float( - (len(options.shifts) * (2 if options.rc else 1)) - ) - - # collect garbage - gc.collect() - - # close files - genome_open.close() - scores_h5.close() - - -def unaugment_grads(grads, fwdrc=False, shift=0): - """Undo sequence augmentation.""" - # reverse complement - if not fwdrc: - # reverse - grads = grads[::-1, :, :] - - # swap A and T - grads[:, [0, 3], :] = grads[:, [3, 0], :] - - # swap C and G - grads[:, [1, 2], :] = grads[:, [2, 1], :] - - # undo shift - if shift < 0: - # shift sequence right - grads[-shift:, :, :] = grads[:shift, :, :] - - # fill in left unknowns - grads[:-shift, :, :] = 0 - - elif shift > 0: - # shift sequence left - grads[:-shift, :, :] = grads[shift:, :, :] - - # fill in right unknowns - grads[-shift:, :, :] = 0 - - return grads - - -def make_seq_1hot(genome_open, chrm, start, end, seq_len): - if start < 0: - seq_dna = "N" * (-start) + genome_open.fetch(chrm, 0, end) - else: - seq_dna = genome_open.fetch(chrm, start, end) - - # extend to full length - if len(seq_dna) < seq_len: - seq_dna += "N" * (seq_len - len(seq_dna)) - - seq_1hot = dna_io.dna_1hot(seq_dna) - return seq_1hot - - -# tf code for predicting raw sum-of-expression counts on GPU -@tf.function -def _count_func( - model, - seq_1hot, - target_slice, - pos_slice, - pos_mask=None, - track_scale=1.0, - track_transform=1.0, - clip_soft=None, - untransform_old=False, - use_mean=False, -): - - # predict - preds = tf.gather( - model(seq_1hot, training=False), target_slice, axis=-1, batch_dims=1 - ) - - if untransform_old: - # undo scale - preds = preds / track_scale - - # undo clip_soft - if clip_soft is not None: - preds = tf.where( - preds > clip_soft, (preds - clip_soft) ** 2 + clip_soft, preds - ) - - # undo sqrt - preds = preds ** (1. / track_transform) - else: - # undo clip_soft - if clip_soft is not None: - preds = tf.where( - preds > clip_soft, (preds - clip_soft + 1) ** 2 + clip_soft - 1, preds - ) - - # undo sqrt - preds = -1 + (preds + 1) ** (1. / track_transform) - - # scale - preds = preds / track_scale - - # aggregate over tracks (average) - preds = tf.reduce_mean(preds, axis=-1) - - # slice specified positions - preds_slice = tf.gather(preds, pos_slice, axis=-1, batch_dims=1) - if pos_mask is not None: - preds_slice = preds_slice * pos_mask - - # aggregate over positions - if not use_mean: - preds_agg = tf.reduce_sum(preds_slice, axis=-1) - else: - if pos_mask is not None: - preds_agg = tf.reduce_sum(preds_slice, axis=-1) / tf.reduce_sum( - pos_mask, axis=-1 - ) - else: - preds_agg = tf.reduce_mean(preds_slice, axis=-1) - - return preds_agg - - -# code for getting model predictions from a tensor of input sequence patterns -def predict_counts( - seqnn_model, - seq_1hot, - head_i=None, - target_slice=None, - pos_slice=None, - pos_mask=None, - chunk_size=None, - batch_size=1, - track_scale=1.0, - track_transform=1.0, - clip_soft=None, - untransform_old=False, - use_mean=False, - dtype="float32", -): - - # start time - t0 = time.time() - - # choose model - if seqnn_model.ensemble is not None: - model = seqnn_model.ensemble - elif head_i is not None: - model = seqnn_model.models[head_i] - else: - model = seqnn_model.model - - # verify tensor shape(s) - seq_1hot = seq_1hot.astype("float32") - target_slice = np.array(target_slice).astype("int32") - pos_slice = np.array(pos_slice).astype("int32") - - # convert constants to tf tensors - track_scale = tf.constant(track_scale, dtype=tf.float32) - track_transform = tf.constant(track_transform, dtype=tf.float32) - if clip_soft is not None: - clip_soft = tf.constant(clip_soft, dtype=tf.float32) - - if pos_mask is not None: - pos_mask = np.array(pos_mask).astype("float32") - - if len(seq_1hot.shape) < 3: - seq_1hot = seq_1hot[None, ...] - - if len(target_slice.shape) < 2: - target_slice = target_slice[None, ...] - - if len(pos_slice.shape) < 2: - pos_slice = pos_slice[None, ...] - - if pos_mask is not None and len(pos_mask.shape) < 2: - pos_mask = pos_mask[None, ...] - - # chunk parameters - num_chunks = 1 - if chunk_size is None: - chunk_size = seq_1hot.shape[0] - else: - num_chunks = int(np.ceil(seq_1hot.shape[0] / chunk_size)) - - # loop over chunks - pred_chunks = [] - for ci in range(num_chunks): - - # collect chunk - seq_1hot_chunk = seq_1hot[ci * chunk_size : (ci + 1) * chunk_size, ...] - target_slice_chunk = target_slice[ci * chunk_size : (ci + 1) * chunk_size, ...] - pos_slice_chunk = pos_slice[ci * chunk_size : (ci + 1) * chunk_size, ...] - - pos_mask_chunk = None - if pos_mask is not None: - pos_mask_chunk = pos_mask[ci * chunk_size : (ci + 1) * chunk_size, ...] - - actual_chunk_size = seq_1hot_chunk.shape[0] - - # convert to tf tensors - seq_1hot_chunk = tf.convert_to_tensor(seq_1hot_chunk, dtype=tf.float32) - target_slice_chunk = tf.convert_to_tensor(target_slice_chunk, dtype=tf.int32) - pos_slice_chunk = tf.convert_to_tensor(pos_slice_chunk, dtype=tf.int32) - - if pos_mask is not None: - pos_mask_chunk = tf.convert_to_tensor(pos_mask_chunk, dtype=tf.float32) - - # batching parameters - num_batches = int(np.ceil(actual_chunk_size / batch_size)) - - # loop over batches - pred_batches = [] - for bi in range(num_batches): - - # collect batch - seq_1hot_batch = seq_1hot_chunk[ - bi * batch_size : (bi + 1) * batch_size, ... - ] - target_slice_batch = target_slice_chunk[ - bi * batch_size : (bi + 1) * batch_size, ... - ] - pos_slice_batch = pos_slice_chunk[ - bi * batch_size : (bi + 1) * batch_size, ... - ] - - pos_mask_batch = None - if pos_mask is not None: - pos_mask_batch = pos_mask_chunk[ - bi * batch_size : (bi + 1) * batch_size, ... - ] - - pred_batch = ( - _count_func( - model, - seq_1hot_batch, - target_slice_batch, - pos_slice_batch, - pos_mask_batch, - track_scale, - track_transform, - clip_soft, - untransform_old, - use_mean, - ) - .numpy() - .astype(dtype) - ) - - pred_batches.append(pred_batch) - - # concat predicted batches - preds = np.concatenate(pred_batches, axis=0) - - pred_chunks.append(preds) - - # collect garbage - gc.collect() - - # concat predicted chunks - preds = np.concatenate(pred_chunks, axis=0) - - print("Made predictions in %ds" % (time.time() - t0)) - - return preds - - -################################################################################ -# __main__ -# ############################################################################### -if __name__ == "__main__": - main() diff --git a/src/scripts/borzoi_satg_polya_gpu.py b/src/scripts/borzoi_satg_polya.py similarity index 98% rename from src/scripts/borzoi_satg_polya_gpu.py rename to src/scripts/borzoi_satg_polya.py index 2b4b8e0..9f26eba 100755 --- a/src/scripts/borzoi_satg_polya_gpu.py +++ b/src/scripts/borzoi_satg_polya.py @@ -25,12 +25,12 @@ import pysam from baskerville.dataset import targets_prep_strand -from baskerville import dna_io +from baskerville import dna as dna_io from baskerville import gene as bgene from baskerville import seqnn """ -borzoi_satg_polya_gpu.py +borzoi_satg_polya.py Perform a gradient saliency analysis for genes specified in a GTF file (polyadenylation-centric). """ @@ -44,7 +44,7 @@ def main(): parser.add_option( "--fa", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( @@ -70,9 +70,9 @@ def main(): parser.add_option( '-c', dest='crosses', - default=1, - type='int', - help='Number of cross-fold rounds [Default:%default]', + default="0", + type="str", + help='Model crosses (replicates) to use in ensemble (comma-separated list) [Default:%default]', ) parser.add_option( "--head", @@ -133,7 +133,7 @@ def main(): parser.add_option( "-a", dest="apa_file", - default="%s/genes/polyadb/polyadb_human_v3.csv.gz" % os.environ["HG38"], + default="%s/genes/polyadb/polyadb_human_v3.csv.gz" % os.environ.get('BORZOI_HG38', 'hg38'), help="Polyadenylation site annotation [Default: %default]", ) (options, args) = parser.parse_args() @@ -147,9 +147,10 @@ def main(): parser.error("Must provide parameter file, model folder and GTF file") if not os.path.isdir(options.out_dir): - os.mkdir(options.out_dir) + os.makedirs(options.out_dir, exist_ok=True) options.folds = [int(fold) for fold in options.folds.split(",")] + options.crosses = [int(cross) for cross in options.crosses.split(",")] options.shifts = [int(shift) for shift in options.shifts.split(",")] ################################################################# diff --git a/src/scripts/borzoi_satg_splice_gpu.py b/src/scripts/borzoi_satg_splice.py similarity index 98% rename from src/scripts/borzoi_satg_splice_gpu.py rename to src/scripts/borzoi_satg_splice.py index 8d01451..473192f 100755 --- a/src/scripts/borzoi_satg_splice_gpu.py +++ b/src/scripts/borzoi_satg_splice.py @@ -25,12 +25,12 @@ import pysam from baskerville.dataset import targets_prep_strand -from baskerville import dna_io +from baskerville import dna as dna_io from baskerville import gene as bgene from baskerville import seqnn """ -borzoi_satg_splice_gpu.py +borzoi_satg_splice.py Perform a gradient saliency analysis for genes specified in a GTF file (splice-centric). """ @@ -44,7 +44,7 @@ def main(): parser.add_option( "--fa", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( @@ -70,9 +70,9 @@ def main(): parser.add_option( '-c', dest='crosses', - default=1, - type='int', - help='Number of cross-fold rounds [Default:%default]', + default="0", + type="str", + help='Model crosses (replicates) to use in ensemble (comma-separated list) [Default:%default]', ) parser.add_option( "--head", @@ -134,7 +134,7 @@ def main(): "-s", dest="splice_gff", default="%s/genes/gencode41/gencode41_basic_protein_splice.gff" - % os.environ["HG38"], + % os.environ.get('BORZOI_HG38', 'hg38'), help="Splice site annotation [Default: %default]", ) (options, args) = parser.parse_args() @@ -148,9 +148,10 @@ def main(): parser.error("Must provide parameter file, model folder and GTF file") if not os.path.isdir(options.out_dir): - os.mkdir(options.out_dir) + os.makedirs(options.out_dir, exist_ok=True) options.folds = [int(fold) for fold in options.folds.split(",")] + options.crosses = [int(cross) for cross in options.crosses.split(",")] options.shifts = [int(shift) for shift in options.shifts.split(",")] ################################################################# diff --git a/src/scripts/borzoi_sed.py b/src/scripts/borzoi_sed.py index dc0a736..353382b 100755 --- a/src/scripts/borzoi_sed.py +++ b/src/scripts/borzoi_sed.py @@ -55,13 +55,13 @@ def main(): parser.add_option( "-f", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( "-g", dest="genes_gtf", - default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ["HG38"], + default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ.get('BORZOI_HG38', 'hg38'), help="GTF for gene definition [Default %default]", ) parser.add_option( diff --git a/src/scripts/borzoi_sed_folds.py b/src/scripts/borzoi_sed_folds.py old mode 100644 new mode 100755 index e7f92a9..02c5ccd --- a/src/scripts/borzoi_sed_folds.py +++ b/src/scripts/borzoi_sed_folds.py @@ -44,13 +44,13 @@ def main(): sed_options.add_option( '-f', dest='genome_fasta', - default='%s/assembly/ucsc/hg38.fa' % os.environ['HG38'], + default='%s/assembly/ucsc/hg38.fa' % os.environ.get('BORZOI_HG38', 'hg38'), help='Genome FASTA for sequences [Default: %default]', ) sed_options.add_option( '-g', dest='genes_gtf', - default='%s/genes/gencode41/gencode41_basic_nort.gtf' % os.environ['HG38'], + default='%s/genes/gencode41/gencode41_basic_nort.gtf' % os.environ.get('BORZOI_HG38', 'hg38'), help='GTF for gene definition [Default %default]', ) sed_options.add_option( @@ -208,8 +208,8 @@ def main(): # SNP scores # command base - cmd_base = '. /home/drk/anaconda3/etc/profile.d/conda.sh;' - cmd_base += ' conda activate %s;' % options.conda_env + cmd_base = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd_base += 'conda activate %s;' % options.conda_env cmd_base += ' echo $HOSTNAME;' jobs = [] diff --git a/src/scripts/borzoi_sed_ipaqtl_cov.py b/src/scripts/borzoi_sed_ipaqtl_cov.py index 9e08f94..74000bc 100755 --- a/src/scripts/borzoi_sed_ipaqtl_cov.py +++ b/src/scripts/borzoi_sed_ipaqtl_cov.py @@ -48,19 +48,20 @@ def main(): parser.add_option( "-f", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( "-g", dest="genes_gtf", - default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ["HG38"], + default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ.get('BORZOI_HG38', 'hg38'), help="GTF for gene definition [Default %default]", ) parser.add_option( "--apafile", dest="apa_file", - default="polyadb_human_v3.csv.gz" + default="%s/genes/polyadb/polyadb_human_v3.csv.gz" % os.environ.get('BORZOI_HG38', 'hg38'), + help="Csv for polya site definition [Default %default]", ) parser.add_option( "-o", diff --git a/src/scripts/borzoi_sed_paqtl_cov.py b/src/scripts/borzoi_sed_paqtl_cov.py index 84b84cc..7027a92 100755 --- a/src/scripts/borzoi_sed_paqtl_cov.py +++ b/src/scripts/borzoi_sed_paqtl_cov.py @@ -48,19 +48,20 @@ def main(): parser.add_option( "-f", dest="genome_fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( "-g", dest="genes_gtf", - default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ["HG38"], + default="%s/genes/gencode41/gencode41_basic_nort.gtf" % os.environ.get('BORZOI_HG38', 'hg38'), help="GTF for gene definition [Default %default]", ) parser.add_option( "--apafile", dest="apa_file", - default="polyadb_human_v3.csv.gz" + default="%s/genes/polyadb/polyadb_human_v3.csv.gz" % os.environ.get('BORZOI_HG38', 'hg38'), + help="Csv for polya site definition [Default %default]", ) parser.add_option( "-o", diff --git a/src/scripts/borzoi_test_apa_polaydb.py b/src/scripts/borzoi_test_apa.py similarity index 97% rename from src/scripts/borzoi_test_apa_polaydb.py rename to src/scripts/borzoi_test_apa.py index eecf01c..21e4179 100755 --- a/src/scripts/borzoi_test_apa_polaydb.py +++ b/src/scripts/borzoi_test_apa.py @@ -28,7 +28,7 @@ from baskerville import seqnn """ -borzoi_test_apa_polaydb.py +borzoi_test_apa.py Measure accuracy at polyadenylation-level. """ @@ -322,16 +322,16 @@ def main(): apa_preds = np.array(apa_preds) # save numpy arrays with values - np.save("%s/apa_targets_polyadb.npy" % options.out_dir, apa_targets) - np.save("%s/apa_preds_polyadb.npy" % options.out_dir, apa_preds) + np.save("%s/apa_targets.npy" % options.out_dir, apa_targets) + np.save("%s/apa_preds.npy" % options.out_dir, apa_preds) # save values apa_targets_df = pd.DataFrame(apa_targets, index=pas_ids) apa_targets_df.to_csv( - "%s/apa_targets_polyadb.tsv.gz" % options.out_dir, sep="\t" + "%s/apa_targets.tsv.gz" % options.out_dir, sep="\t" ) apa_preds_df = pd.DataFrame(apa_preds, index=pas_ids) - apa_preds_df.to_csv("%s/apa_preds_polyadb.tsv.gz" % options.out_dir, sep="\t") + apa_preds_df.to_csv("%s/apa_preds.tsv.gz" % options.out_dir, sep="\t") ################################################################################ diff --git a/src/scripts/borzoi_test_apa_folds_polaydb.py b/src/scripts/borzoi_test_apa_folds.py similarity index 93% rename from src/scripts/borzoi_test_apa_folds_polaydb.py rename to src/scripts/borzoi_test_apa_folds.py index 423bb41..ba4fbbb 100755 --- a/src/scripts/borzoi_test_apa_folds_polaydb.py +++ b/src/scripts/borzoi_test_apa_folds.py @@ -20,7 +20,7 @@ import slurm """ -borzoi_test_apa_folds_polaydb.py +borzoi_test_apa_folds.py Measure accuracy at polyadenylation-level for multiple model replicates. """ @@ -67,7 +67,8 @@ def main(): parser.add_option( "-g", dest="apa_file", - default="polyadb_human_v3.csv.gz" + default="%s/genes/polyadb/polyadb_human_v3.csv.gz" % os.environ.get('BORZOI_HG38', 'hg38'), + help="Csv for polya site definition [Default %default]", ) parser.add_option( "--name", @@ -172,15 +173,15 @@ def main(): model_file = "%s/train/model%d_best.h5" % (it_dir, options.dataset_i) # check if done - acc_file = "%s/apa_preds_polyadb.tsv.gz" % out_dir + acc_file = "%s/apa_preds.tsv.gz" % out_dir if os.path.isfile(acc_file): # print('%s already generated.' % acc_file) pass else: # evaluate - cmd = ". /home/drk/anaconda3/etc/profile.d/conda.sh;" - cmd += " conda activate %s;" % options.conda_env - cmd += " time borzoi_test_apa_polaydb.py" + cmd = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd += "conda activate %s;" % options.conda_env + cmd += " time borzoi_test_apa.py" cmd += " --head %d" % head_i cmd += " -o %s" % out_dir if options.rc: diff --git a/src/scripts/borzoi_test_exons.py b/src/scripts/borzoi_test_exons.py index fe63e62..a599059 100755 --- a/src/scripts/borzoi_test_exons.py +++ b/src/scripts/borzoi_test_exons.py @@ -99,6 +99,13 @@ def main(): default=None, help="TFR pattern string appended to data_dir/tfrecords for subsetting [Default: %default]", ) + parser.add_option( + "-u", + dest="untransform_old", + default=False, + action="store_true", + help="Untransform old models [Default: %default]", + ) (options, args) = parser.parse_args() if len(args) != 4: @@ -235,7 +242,12 @@ def main(): # predict only if gene overlaps yh = None y = y.numpy()[..., targets_df.index] - y = dataset.untransform_preds1(y, targets_df, unscale=True) + + # untransform + if options.untransform_old: + y = dataset.untransform_preds1(y, targets_df, unscale=True) + else: + y = dataset.untransform_preds(y, targets_df, unscale=True) t0 = time.time() print("Sequence %d..." % si, end="") @@ -268,7 +280,13 @@ def main(): if yh is None: yh = seqnn_model(x) print(yh.max(), " untransformed to ", end="") - yh = dataset.untransform_preds1(yh, targets_df, unscale=True) + + # untransform + if options.untransform_old: + yh = dataset.untransform_preds1(yh, targets_df, unscale=True) + else: + yh = dataset.untransform_preds(yh, targets_df, unscale=True) + print(yh.max()) # slice gene region diff --git a/src/scripts/borzoi_test_exons_folds.py b/src/scripts/borzoi_test_exons_folds.py index 7091465..93aaf40 100755 --- a/src/scripts/borzoi_test_exons_folds.py +++ b/src/scripts/borzoi_test_exons_folds.py @@ -104,7 +104,7 @@ def main(): "-g", dest="exons_gff", default="%s/genes/gencode41/gencode41_basic_nort_protein_exons.gff" - % os.environ["HG38"], + % os.environ.get('BORZOI_HG38', 'hg38'), ) parser.add_option( "--label_exp", @@ -137,9 +137,16 @@ def main(): help="Output experiment directory [Default: %default]", ) parser.add_option( - "-p", dest="out_stem", default=None, help="Output plot stem [Default: %default]" + "-p", + dest="out_stem", + default=None, + help="Output plot stem [Default: %default]" + ) + parser.add_option( + "-q", + dest="queue", + default="geforce" ) - parser.add_option("-q", dest="queue", default="geforce") parser.add_option( "-r", dest="ref_dir", @@ -160,13 +167,6 @@ def main(): type="str", help="Ensemble prediction shifts [Default: %default]", ) - parser.add_option( - "--status", - dest="status", - default=False, - action="store_true", - help="Update metric status; do not run jobs [Default: %default]", - ) parser.add_option( "-t", dest="targets_file", @@ -174,6 +174,13 @@ def main(): type="str", help="File specifying target indexes and labels in table format", ) + parser.add_option( + '-u', + dest='untransform_old', + default=False, + action='store_true', + help='Untransform old models [Default: %default]', + ) (options, args) = parser.parse_args() if len(args) < 2: @@ -238,8 +245,8 @@ def main(): pass else: # evaluate - cmd = ". /home/drk/anaconda3/etc/profile.d/conda.sh;" - cmd += " conda activate %s;" % options.conda_env + cmd = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd += "conda activate %s;" % options.conda_env cmd += " time borzoi_test_exons.py" cmd += " --head %d" % head_i cmd += " -o %s" % out_dir @@ -249,6 +256,11 @@ def main(): cmd += " --shifts %s" % options.shifts if options.targets_file is not None: cmd += " -t %s" % options.targets_file + if options.exons_bed is not None: + cmd += " -b %s" % options.exons_bed + if options.untransform_old: + cmd += " -u" + cmd += " -e %d" % options.exon_end cmd += " %s" % params_file cmd += " %s" % model_file cmd += " %s/data%d" % (it_dir, head_i) diff --git a/src/scripts/borzoi_test_genes.py b/src/scripts/borzoi_test_genes.py index bfdb2aa..8a7c4b9 100755 --- a/src/scripts/borzoi_test_genes.py +++ b/src/scripts/borzoi_test_genes.py @@ -425,7 +425,7 @@ def main(): ) acc_nr2.append(nr2_ti) var_mask = gene_wvar[:, ti] > wvar_t[ti] - wr_ti = gene_within[var_mask].mean() + wr_ti = gene_within[:, ti][var_mask].mean() acc_wpearsonr.append(wr_ti) acc_df = pd.DataFrame( diff --git a/src/scripts/borzoi_test_genes_folds.py b/src/scripts/borzoi_test_genes_folds.py index b558205..332a0fe 100755 --- a/src/scripts/borzoi_test_genes_folds.py +++ b/src/scripts/borzoi_test_genes_folds.py @@ -148,7 +148,7 @@ def main(): parser.add_option( "-g", dest="genes_gtf", - default="%s/genes/gencode41/gencode41_basic_protein.gtf" % os.environ["HG38"], + default="%s/genes/gencode41/gencode41_basic_protein.gtf" % os.environ.get('BORZOI_HG38', 'hg38'), ) parser.add_option( "--label_exp", @@ -268,8 +268,8 @@ def main(): pass else: # evaluate - cmd = ". /home/drk/anaconda3/etc/profile.d/conda.sh;" - cmd += " conda activate %s;" % options.conda_env + cmd = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd += "conda activate %s;" % options.conda_env cmd += " time borzoi_test_genes.py" cmd += ' --head %d' % head_i cmd += " -o %s" % out_dir diff --git a/src/scripts/borzoi_test_tss_gencode.py b/src/scripts/borzoi_test_tss.py old mode 100644 new mode 100755 similarity index 96% rename from src/scripts/borzoi_test_tss_gencode.py rename to src/scripts/borzoi_test_tss.py index 3e88a02..ac1eb3d --- a/src/scripts/borzoi_test_tss_gencode.py +++ b/src/scripts/borzoi_test_tss.py @@ -28,7 +28,7 @@ from baskerville import seqnn ''' -borzoi_test_tss_gencode.py +borzoi_test_tss.py Measure accuracy at TSS-level. ''' @@ -309,14 +309,14 @@ def main(): tss_preds = np.array(tss_preds) # save numpy arrays with values - np.save('%s/tss_targets_gencode.npy' % options.out_dir, tss_targets) - np.save('%s/tss_preds_gencode.npy' % options.out_dir, tss_preds) + np.save('%s/tss_targets.npy' % options.out_dir, tss_targets) + np.save('%s/tss_preds.npy' % options.out_dir, tss_preds) # save values tss_targets_df = pd.DataFrame(tss_targets, index=tss_ids) - tss_targets_df.to_csv('%s/tss_targets_gencode.tsv.gz' % options.out_dir, sep='\t') + tss_targets_df.to_csv('%s/tss_targets.tsv.gz' % options.out_dir, sep='\t') tss_preds_df = pd.DataFrame(tss_preds, index=tss_ids) - tss_preds_df.to_csv('%s/tss_preds_gencode.tsv.gz' % options.out_dir, sep='\t') + tss_preds_df.to_csv('%s/tss_preds.tsv.gz' % options.out_dir, sep='\t') ################################################################################ # __main__ diff --git a/src/scripts/borzoi_test_tss_folds_gencode.py b/src/scripts/borzoi_test_tss_folds.py old mode 100644 new mode 100755 similarity index 94% rename from src/scripts/borzoi_test_tss_folds_gencode.py rename to src/scripts/borzoi_test_tss_folds.py index 1b65130..3fc4fed --- a/src/scripts/borzoi_test_tss_folds_gencode.py +++ b/src/scripts/borzoi_test_tss_folds.py @@ -20,7 +20,7 @@ import slurm """ -borzoi_test_tss_folds_gencode.py +borzoi_test_tss_folds.py Measure accuracy at TSS-level for multiple model replicates. """ @@ -67,7 +67,8 @@ def main(): parser.add_option( '-g', dest='tss_file', - default='/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_tss2.bed', + default='%s/genes/gencode41/gencode41_basic_tss2.bed' % os.environ.get('BORZOI_HG38', 'hg38'), + help='Bed for tss definition [Default %default]', ) parser.add_option( '--name', @@ -194,15 +195,15 @@ def main(): model_file = '%s/train/model%d_best.h5' % (it_dir, options.dataset_i) # check if done - acc_file = '%s/tss_preds_gencode.tsv.gz' % out_dir + acc_file = '%s/tss_preds.tsv.gz' % out_dir if os.path.isfile(acc_file): # print('%s already generated.' % acc_file) pass else: # evaluate - cmd = '. /home/drk/anaconda3/etc/profile.d/conda.sh;' - cmd += ' conda activate %s;' % options.conda_env - cmd += ' time borzoi_test_tss_gencode.py' + cmd = ('. %s; ' % os.environ['BORZOI_CONDA']) if 'BORZOI_CONDA' in os.environ else '' + cmd += 'conda activate %s;' % options.conda_env + cmd += ' time borzoi_test_tss.py' cmd += ' --head %d' % head_i cmd += ' -o %s' % out_dir if options.rc: diff --git a/src/scripts/borzoi_tfmodisco.py b/src/scripts/borzoi_tfmodisco.py old mode 100644 new mode 100755 index 4caa384..6433461 --- a/src/scripts/borzoi_tfmodisco.py +++ b/src/scripts/borzoi_tfmodisco.py @@ -43,13 +43,13 @@ def main(): parser.add_option( '-d', dest='meme_db', - default='/homde/drk/code/meme-5.4.1/motif_databases/CIS-BP_2.00/Homo_sapiens.meme', + default='meme-5.4.1/motif_databases/CIS-BP_2.00/Homo_sapiens.meme', help='Meme database [Default: %default]', ) parser.add_option( '-g', dest='genes_gtf_file', - default='/home/drk/common/data/genomes/hg38/genes/gencode38/gencode38_basic_protein.gtf', + default='%s/genes/gencode38/gencode38_basic_protein.gtf' % os.environ.get('BORZOI_HG38', 'hg38'), help='Gencode GTF [Default: %default]', ) parser.add_option( @@ -361,7 +361,7 @@ def main(): modisco_meme_open.close() # run tomtom - tomtom_cmd = '/home/drk/bin/tomtom -dist pearson -thresh 0.1 -oc %s %s %s' % \ + tomtom_cmd = 'tomtom -dist pearson -thresh 0.1 -oc %s %s %s' % \ (options.out_dir, modisco_meme_file, options.meme_db) subprocess.call(tomtom_cmd, shell=True) diff --git a/src/scripts/borzoi_tfmodisco_diff.py b/src/scripts/borzoi_tfmodisco_diff.py old mode 100644 new mode 100755 index a0119f9..b97fe20 --- a/src/scripts/borzoi_tfmodisco_diff.py +++ b/src/scripts/borzoi_tfmodisco_diff.py @@ -45,13 +45,13 @@ def main(): parser.add_option( '-d', dest='meme_db', - default='/homde/drk/code/meme-5.4.1/motif_databases/CIS-BP_2.00/Homo_sapiens.meme', + default='meme-5.4.1/motif_databases/CIS-BP_2.00/Homo_sapiens.meme', help='Meme database [Default: %default]', ) parser.add_option( '-g', dest='genes_gtf_file', - default='/home/drk/common/data/genomes/hg38/genes/gencode38/gencode38_basic_protein.gtf', + default='%s/genes/gencode38/gencode38_basic_protein.gtf' % os.environ.get('BORZOI_HG38', 'hg38'), help='Gencode GTF [Default: %default]', ) parser.add_option( @@ -401,7 +401,7 @@ def main(): modisco_meme_open.close() # run tomtom - tomtom_cmd = '/home/drk/bin/tomtom -dist pearson -thresh 0.1 -oc %s %s %s' % \ + tomtom_cmd = 'tomtom -dist pearson -thresh 0.1 -oc %s %s %s' % \ (options.out_dir, modisco_meme_file, options.meme_db) subprocess.call(tomtom_cmd, shell=True) diff --git a/src/scripts/borzoi_trip.py b/src/scripts/borzoi_trip.py index 0d84ac5..64fccd9 100755 --- a/src/scripts/borzoi_trip.py +++ b/src/scripts/borzoi_trip.py @@ -24,7 +24,7 @@ import pandas as pd import pysam -from baskerville import dna_io +from baskerville import dna as dna_io from baskerville import seqnn from baskerville import stream @@ -48,7 +48,7 @@ def main(): parser.add_option( "-f", dest="fasta", - default="%s/assembly/ucsc/hg38.fa" % os.environ["HG38"], + default="%s/assembly/ucsc/hg38.fa" % os.environ.get('BORZOI_HG38', 'hg38'), help="Genome FASTA for sequences [Default: %default]", ) parser.add_option( diff --git a/src/scripts/bw_h5.py b/src/scripts/bw_h5.py new file mode 100755 index 0000000..2780016 --- /dev/null +++ b/src/scripts/bw_h5.py @@ -0,0 +1,140 @@ +#!/usr/bin/env python +from optparse import OptionParser +import sys + +import h5py +import numpy as np +import pyBigWig +import scipy.interpolate + +''' +bw_h5.py + +Convert a BigWig to HDF5. +''' + +################################################################################ +# main +################################################################################ +def main(): + usage = 'usage: %prog [options] ' + parser = OptionParser(usage) + parser.add_option('-c', '--chr_strip', dest='chr_strip', + default=False, action='store_true') + parser.add_option('-i', dest='interp_nan', + default=False, action='store_true', + help='Interpolate NaNs [Default: %default]') + parser.add_option('-m', dest='min_norm', + default=False, action='store_true', + help='Normalize the minimum nonzero value to 1 [Default: %default]') + # parser.add_option('--mode_max', dest='mode_norm_max', + # default=10, type='float', + # help='Maximum norm scale value determined by mode [Default: %default]') + parser.add_option('-s', dest='scale', + default=1.0, type='float', + help='Scale all values (e.g. to undo normalization) [Default: %default]') + parser.add_option('-v', dest='verbose', + default=False, action='store_true') + parser.add_option('-z', dest='clip_zero', + default=False, action='store_true', + help='Clip negative values at zero [Default: %default]') + (options,args) = parser.parse_args() + + if len(args) != 2: + parser.error('Must provide input BigWig and output HDF5.') + else: + bw_file = args[0] + hdf5_file = args[1] + + # open files + bw_in = pyBigWig.open(bw_file) + h5_out = h5py.File(hdf5_file, 'w') + + # process chromosomes in length order + chrom_lengths = bw_in.chroms() + chroms = sorted(chrom_lengths.keys()) + length_chroms = [(chrom_lengths[chrm],chrm) for chrm in chroms] + length_chroms = sorted(length_chroms)[::-1] + min_factor = None + + # for each chromosome + for clength, chrom in length_chroms: + if options.verbose: + print(chrom) + + # read values + x = bw_in.values(chrom, 0, chrom_lengths[chrom], numpy=True) + + # scale + if options.scale != 1: + x = x*options.scale + + if options.min_norm: + if min_factor is None: + min_factor = x[x>0].min() + # vals, counts = np.unique(x[x>0], return_counts=True) + # mode_factor = vals[0] + # mode_factor = np.clip(vals[0], 1/options.mode_norm_max, options.mode_norm_max) + print('Min normalization factor: %f' % min_factor, file=sys.stderr) + x /= min_factor + + # interpolate NaN + if options.interp_nan: + x = interp_nan(x) + else: + x = np.nan_to_num(x) + + # clip negative values + if options.clip_zero: + x = np.clip(x, 0, np.inf) + + # clip float16 min/max + x = np.clip(x, np.finfo(np.float16).min, np.finfo(np.float16).max) + + # strip "chr" + if options.chr_strip: + chrom = chrom.replace('chr','') + + # write gzipped into HDF5 + x = x.astype('float16') + h5_out.create_dataset(chrom, data=x, dtype='float16', compression='gzip', shuffle=True) + + # close files + h5_out.close() + bw_in.close() + + +def interp_nan(x, kind='linear'): + '''Linearly interpolate to fill NaN.''' + + # pad zeroes + xp = np.zeros(len(x)+2) + xp[1:-1] = x + + # find NaN + x_nan = np.isnan(xp) + + if np.sum(x_nan) == 0: + # unnecessary + return x + + else: + # interpolate + inds = np.arange(len(xp)) + interpolator = scipy.interpolate.interp1d( + inds[~x_nan], + xp[~x_nan], + kind=kind, + bounds_error=False) + + loc = np.where(x_nan) + xp[loc] = interpolator(loc) + + # slice off pad + return xp[1:-1] + +################################################################################ +# __main__ +################################################################################ +if __name__ == '__main__': + main() diff --git a/src/scripts/data/qtl_data/README.md b/src/scripts/data/qtl_data/README.md deleted file mode 100644 index 8831abf..0000000 --- a/src/scripts/data/qtl_data/README.md +++ /dev/null @@ -1,33 +0,0 @@ -## QTL data processing - -The scripts in this folder are used to extract fine-mapped causal sQTLs, paQTLs and ipaQTLs from the results of the eQTL Catalogue, as well as construct distance- and expression-matched negative SNPs.
- -*Notes*: -- The pipeline requires the GTEx v8 (median) TPM matrix, which can be downloaded [here](https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz). -
- -As a prerequisite to generating any of the QTL datasets, run the following scripts (in order): -1. download_finemap.py -2. download_sumstat.py -3. merge_finemapping_tables.py -4. make_expression_tables.py -
- -To prepare the sQTL dataset, run these scripts: -1. sqtl_make_positive_sets.py -2. sqtl_make_negative_sets.py -
- -To prepare the paQTL dataset, run these scripts: -1. paqtl_make_positive_sets.py -2. paqtl_make_negative_sets.py -
- -To prepare the ipaQTL dataset, run these scripts: -1. ipaqtl_make_positive_sets.py -2. ipaqtl_make_negative_sets.py -
- -Finally, to generate the QTL VCF files, run this script: -1. make_vcfs.py -
diff --git a/src/scripts/data/qtl_data/download_finemap.py b/src/scripts/data/qtl_data/download_finemap.py deleted file mode 100644 index 558e3ef..0000000 --- a/src/scripts/data/qtl_data/download_finemap.py +++ /dev/null @@ -1,62 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import pandas as pd - -import util - -''' -download_finemap.py - -Download QTL Catalogue fine-mapping results. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - # read remote table - samples_df = pd.read_csv('https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv', sep='\t') - - # filter GTEx (for now) - samples_df = samples_df[samples_df.study == 'GTEx'] - - - ################################################ - # txrevise for splicing / polyA / TSS QTLs - - os.makedirs('txrev', exist_ok=True) - txrev_df = samples_df[samples_df.quant_method == 'txrev'] - - jobs = [] - for all_ftp_path in txrev_df.ftp_path: - # ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/Alasoo_2018/txrev/Alasoo_2018_txrev_macrophage_IFNg+Salmonella.all.tsv.gz - # ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/credible_sets//Alasoo_2018_txrev_macrophage_IFNg+Salmonella.purity_filtered.txt.gz - - all_ftp_file = all_ftp_path.split('/')[-1] - fine_ftp_file = all_ftp_file.replace('all.tsv', 'purity_filtered.txt') - - fine_ftp_path = 'ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/credible_sets/' - fine_ftp_path += fine_ftp_file - - local_path = 'txrev/%s' % fine_ftp_file - if not os.path.isfile(local_path): - cmd = 'curl -o %s %s' % (local_path, fine_ftp_path) - jobs.append(cmd) - - util.exec_par(jobs, 4, verbose=True) - # print('\n'.join(jobs)) - - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/download_sumstat.py b/src/scripts/data/qtl_data/download_sumstat.py deleted file mode 100644 index ca402df..0000000 --- a/src/scripts/data/qtl_data/download_sumstat.py +++ /dev/null @@ -1,56 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import pandas as pd - -import util - -''' -download_sumstat.py - -Download QTL Catalogue sumstats. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - # read remote table - samples_df = pd.read_csv('https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv', sep='\t') - - # filter GTEx (for now) - samples_df = samples_df[samples_df.study == 'GTEx'] - - - ################################################ - # ge for sumstat (we want SNPs and possibly also base expression) - - os.makedirs('ge', exist_ok=True) - txrev_df = samples_df[samples_df.quant_method == 'ge'] - - jobs = [] - for all_ftp_path in txrev_df.ftp_path: - # ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/Alasoo_2018/txrev/Alasoo_2018_txrev_macrophage_IFNg+Salmonella.all.tsv.gz - - local_path = 'ge/%s' % all_ftp_path.split("/")[-1] - - if not os.path.isfile(local_path): - cmd = 'curl -o %s %s' % (local_path, all_ftp_path) - jobs.append(cmd) - - util.exec_par(jobs, 4, verbose=True) - # print('\n'.join(jobs)) - - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/ipaqtl_make_negative_sets.py b/src/scripts/data/qtl_data/ipaqtl_make_negative_sets.py deleted file mode 100644 index 3f4d49d..0000000 --- a/src/scripts/data/qtl_data/ipaqtl_make_negative_sets.py +++ /dev/null @@ -1,196 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -import pyranges as pr - -''' -paqtl_make_negative_sets.py - -Build tables with negative (non-causal) SNPs for paQTLs. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Parameters - pip_cutoff = 0.01 - max_distance = 10000 - gene_pad = 50 - apa_file = 'polyadb_intron.bed' - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort.gtf' - finemap_file = 'txrev/GTEx_txrev_finemapped_merged.csv.gz' - - #Define tissues - tissue_names = [ - 'adipose_subcutaneous', - 'adipose_visceral', - 'adrenal_gland', - 'artery_aorta', - 'artery_coronary', - 'artery_tibial', - 'blood', - 'brain_amygdala', - 'brain_anterior_cingulate_cortex', - 'brain_caudate', - 'brain_cerebellar_hemisphere', - 'brain_cerebellum', - 'brain_cortex', - 'brain_frontal_cortex', - 'brain_hippocampus', - 'brain_hypothalamus', - 'brain_nucleus_accumbens', - 'brain_putamen', - 'brain_spinal_cord', - 'brain_substantia_nigra', - 'breast', - 'colon_sigmoid', - 'colon_transverse', - 'esophagus_gej', - 'esophagus_mucosa', - 'esophagus_muscularis', - 'fibroblast', - 'heart_atrial_appendage', - 'heart_left_ventricle', - 'kidney_cortex', - 'LCL', - 'liver', - 'lung', - 'minor_salivary_gland', - 'muscle', - 'nerve_tibial', - 'ovary', - 'pancreas', - 'pituitary', - 'prostate', - 'skin_not_sun_exposed', - 'skin_sun_exposed', - 'small_intestine', - 'spleen', - 'stomach', - 'testis', - 'thyroid', - 'uterus', - 'vagina', - ] - - #Compile negative SNP set for each tissue - for tissue_name in tissue_names : - - print("-- " + str(tissue_name) + " --") - - #Load summary stats and extract unique set of SNPs - vcf_df = pd.read_csv("ge/GTEx_ge_" + tissue_name + ".all.tsv.gz", sep='\t', compression='gzip', usecols=['chromosome', 'position', 'ref', 'alt']).drop_duplicates(subset=['chromosome', 'position', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - - #Only keep SNPs (no indels) - vcf_df = vcf_df.loc[(vcf_df['ref'].str.len() == vcf_df['alt'].str.len()) & (vcf_df['ref'].str.len() == 1)].copy().reset_index(drop=True) - - vcf_df['chromosome'] = 'chr' + vcf_df['chromosome'].astype(str) - vcf_df['start'] = vcf_df['position'].astype(int) - vcf_df['end'] = vcf_df['start'] + 1 - vcf_df['strand'] = "." - - vcf_df = vcf_df[['chromosome', 'start', 'end', 'ref', 'alt', 'strand']] - vcf_df = vcf_df.rename(columns={'chromosome' : 'Chromosome', 'start' : 'Start', 'end' : 'End', 'strand' : 'Strand'}) - - print("len(vcf_df) = " + str(len(vcf_df))) - - #Store intermediate SNPs - #vcf_df.to_csv("ge/GTEx_snps_" + tissue_name + ".bed.gz", sep='\t', index=False, header=False) - - #Load polyadenylation site annotation - apa_df = pd.read_csv(apa_file, sep='\t', names=['Chromosome', 'Start', 'End', 'pas_id', 'feat1', 'Strand']) - apa_df['Start'] += 1 - - #Load gene span annotation - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str']) - gtf_df = gtf_df.query("feature == 'gene'").copy().reset_index(drop=True) - - gtf_df['gene_id'] = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]) - - gtf_df = gtf_df[['Chromosome', 'Start', 'End', 'gene_id', 'feat1', 'Strand']].drop_duplicates(subset=['gene_id'], keep='first').copy().reset_index(drop=True) - - gtf_df['Start'] = gtf_df['Start'].astype(int) - gene_pad - gtf_df['End'] = gtf_df['End'].astype(int) + gene_pad - - #Join dataframes against gtf annotation - apa_pr = pr.PyRanges(apa_df) - gtf_pr = pr.PyRanges(gtf_df) - vcf_pr = pr.PyRanges(vcf_df) - - apa_gtf_pr = apa_pr.join(gtf_pr, strandedness='same') - vcf_gtf_pr = vcf_pr.join(gtf_pr, strandedness=False) - - apa_gtf_df = apa_gtf_pr.df[['Chromosome', 'Start', 'End', 'pas_id', 'gene_id', 'Strand']].copy().reset_index(drop=True) - vcf_gtf_df = vcf_gtf_pr.df[['Chromosome', 'Start', 'End', 'ref', 'alt', 'Strand', 'gene_id']].copy().reset_index(drop=True) - - apa_gtf_df['Start'] -= max_distance - apa_gtf_df['End'] += max_distance - - #Join vcf against polyadenylation annotation - apa_gtf_pr = pr.PyRanges(apa_gtf_df) - vcf_gtf_pr = pr.PyRanges(vcf_gtf_df) - - vcf_apa_pr = vcf_gtf_pr.join(apa_gtf_pr, strandedness=False) - - #Force gene_id of SNP to be same as the gene_id of the polyA site - vcf_apa_df = vcf_apa_pr.df.query("gene_id == gene_id_b").copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df[['Chromosome', 'Start', 'ref', 'alt', 'gene_id', 'pas_id', 'Strand_b', 'Start_b']] - - #PolyA site position - vcf_apa_df['Start_b'] += max_distance - vcf_apa_df = vcf_apa_df.rename(columns={'Start' : 'Pos', 'Start_b' : 'pas_pos', 'Strand_b' : 'Strand'}) - - #Distance to polyA site - vcf_apa_df['distance'] = np.abs(vcf_apa_df['Pos'] - vcf_apa_df['pas_pos']) - - #Choose unique SNPs by shortest distance to polyA site - vcf_apa_df = vcf_apa_df.sort_values(by='distance', ascending=True).drop_duplicates(subset=['Chromosome', 'Pos', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df.sort_values(['Chromosome', 'Pos', 'alt'], ascending=True).copy().reset_index(drop=True) - - vcf_df_filtered = vcf_apa_df.rename(columns={'Chromosome' : 'chrom', 'Pos' : 'pos', 'Strand' : 'strand'}) - vcf_df_filtered = vcf_df_filtered[['chrom', 'pos', 'ref', 'alt', 'gene_id', 'pas_id', 'strand', 'pas_pos', 'distance']] - - print("len(vcf_df_filtered) = " + str(len(vcf_df_filtered))) - - #Store intermediate SNPs (filtered) - vcf_df_filtered.to_csv("ge/GTEx_snps_" + tissue_name + "_intronic_polya_filtered.bed.gz", sep='\t', index=False) - - #Reload filtered SNP file - vcf_df_filtered = pd.read_csv("ge/GTEx_snps_" + tissue_name + "_intronic_polya_filtered.bed.gz", sep='\t', compression='gzip') - - #Create variant identifier - vcf_df_filtered['variant'] = vcf_df_filtered['chrom'] + "_" + vcf_df_filtered['pos'].astype(str) + "_" + vcf_df_filtered['ref'] + "_" + vcf_df_filtered['alt'] - - #Load merged fine-mapping dataframe - finemap_df = pd.read_csv(finemap_file, sep='\t')[['variant', 'pip']] - - #Join against fine-mapping dataframe - neg_df = vcf_df_filtered.join(finemap_df.set_index('variant'), on='variant', how='left') - neg_df.loc[neg_df['pip'].isnull(), 'pip'] = 0. - - #Only keep SNPs with PIP < cutoff - neg_df = neg_df.query("pip < " + str(pip_cutoff)).copy().reset_index(drop=True) - - #Store final table of negative SNPs - neg_df.to_csv("ge/GTEx_snps_" + tissue_name + "_intronic_polya_negatives.bed.gz", sep='\t', index=False) - - print("len(neg_df) = " + str(len(neg_df))) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/ipaqtl_make_positive_sets.py b/src/scripts/data/qtl_data/ipaqtl_make_positive_sets.py deleted file mode 100644 index f1afb7b..0000000 --- a/src/scripts/data/qtl_data/ipaqtl_make_positive_sets.py +++ /dev/null @@ -1,191 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -import pyranges as pr - -''' -paqtl_make_positive_sets.py - -Build tables with positive (causal) SNPs for paQTLs. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Parameters - pip_cutoff = 0.01 - max_distance = 10000 - gene_pad = 50 - apa_file = 'polyadb_intron.bed' - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort.gtf' - - #Define tissues - tissue_names = [ - 'adipose_subcutaneous', - 'adipose_visceral', - 'adrenal_gland', - 'artery_aorta', - 'artery_coronary', - 'artery_tibial', - 'blood', - 'brain_amygdala', - 'brain_anterior_cingulate_cortex', - 'brain_caudate', - 'brain_cerebellar_hemisphere', - 'brain_cerebellum', - 'brain_cortex', - 'brain_frontal_cortex', - 'brain_hippocampus', - 'brain_hypothalamus', - 'brain_nucleus_accumbens', - 'brain_putamen', - 'brain_spinal_cord', - 'brain_substantia_nigra', - 'breast', - 'colon_sigmoid', - 'colon_transverse', - 'esophagus_gej', - 'esophagus_mucosa', - 'esophagus_muscularis', - 'fibroblast', - 'heart_atrial_appendage', - 'heart_left_ventricle', - 'kidney_cortex', - 'LCL', - 'liver', - 'lung', - 'minor_salivary_gland', - 'muscle', - 'nerve_tibial', - 'ovary', - 'pancreas', - 'pituitary', - 'prostate', - 'skin_not_sun_exposed', - 'skin_sun_exposed', - 'small_intestine', - 'spleen', - 'stomach', - 'testis', - 'thyroid', - 'uterus', - 'vagina', - ] - - #Compile positive SNP set for each tissue - for tissue_name in tissue_names : - - print("-- " + str(tissue_name) + " --") - - #Load fine-mapping table - vcf_df = pd.read_csv("txrev/GTEx_txrev_" + tissue_name + ".purity_filtered.txt.gz", sep='\t', usecols=['chromosome', 'position', 'ref', 'alt', 'variant', 'pip', 'molecular_trait_id'], low_memory=False) - - #Only keep SNPs (no indels) - vcf_df = vcf_df.loc[(vcf_df['ref'].str.len() == vcf_df['alt'].str.len()) & (vcf_df['ref'].str.len() == 1)].copy().reset_index(drop=True) - - #Only keep SNPs associated with polyadenylation events - vcf_df = vcf_df.loc[vcf_df['molecular_trait_id'].str.contains(".downstream.")].copy().reset_index(drop=True) - - vcf_df['chromosome'] = 'chr' + vcf_df['chromosome'].astype(str) - vcf_df['start'] = vcf_df['position'].astype(int) - vcf_df['end'] = vcf_df['start'] + 1 - vcf_df['strand'] = "." - - vcf_df = vcf_df[['chromosome', 'start', 'end', 'ref', 'alt', 'strand', 'variant', 'pip', 'molecular_trait_id']] - vcf_df = vcf_df.rename(columns={'chromosome' : 'Chromosome', 'start' : 'Start', 'end' : 'End', 'strand' : 'Strand'}) - - print("len(vcf_df) = " + str(len(vcf_df))) - - #Load polyadenylation site annotation - apa_df = pd.read_csv(apa_file, sep='\t', names=['Chromosome', 'Start', 'End', 'pas_id', 'feat1', 'Strand']) - apa_df['Start'] += 1 - - #Load gene span annotation - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str']) - gtf_df = gtf_df.query("feature == 'gene'").copy().reset_index(drop=True) - - gtf_df['gene_id'] = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]) - - gtf_df = gtf_df[['Chromosome', 'Start', 'End', 'gene_id', 'feat1', 'Strand']].drop_duplicates(subset=['gene_id'], keep='first').copy().reset_index(drop=True) - - gtf_df['Start'] = gtf_df['Start'].astype(int) - gene_pad - gtf_df['End'] = gtf_df['End'].astype(int) + gene_pad - - #Join dataframes against gtf annotation - apa_pr = pr.PyRanges(apa_df) - gtf_pr = pr.PyRanges(gtf_df) - vcf_pr = pr.PyRanges(vcf_df) - - apa_gtf_pr = apa_pr.join(gtf_pr, strandedness='same') - vcf_gtf_pr = vcf_pr.join(gtf_pr, strandedness=False) - - apa_gtf_df = apa_gtf_pr.df[['Chromosome', 'Start', 'End', 'pas_id', 'gene_id', 'Strand']].copy().reset_index(drop=True) - vcf_gtf_df = vcf_gtf_pr.df[['Chromosome', 'Start', 'End', 'ref', 'alt', 'Strand', 'gene_id', 'variant', 'pip', 'molecular_trait_id']].copy().reset_index(drop=True) - - apa_gtf_df['Start'] -= max_distance - apa_gtf_df['End'] += max_distance - - #Join vcf against polyadenylation annotation - apa_gtf_pr = pr.PyRanges(apa_gtf_df) - vcf_gtf_pr = pr.PyRanges(vcf_gtf_df) - - vcf_apa_pr = vcf_gtf_pr.join(apa_gtf_pr, strandedness=False) - - #Force gene_id of SNP to be same as the gene_id of the polyA site - vcf_apa_df = vcf_apa_pr.df.query("gene_id == gene_id_b").copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df[['Chromosome', 'Start', 'ref', 'alt', 'gene_id', 'pas_id', 'Strand_b', 'Start_b', 'variant', 'pip', 'molecular_trait_id']] - - #Force gene_id of SNP to be same as the gene_id of the finemapped molecular trait - vcf_apa_df['molecular_trait_gene_id'] = vcf_apa_df['molecular_trait_id'].apply(lambda x: x.split(".")[0]) - vcf_apa_df = vcf_apa_df.query("gene_id == molecular_trait_gene_id").copy().reset_index(drop=True) - - #PolyA site position - vcf_apa_df['Start_b'] += max_distance - vcf_apa_df = vcf_apa_df.rename(columns={'Start' : 'Pos', 'Start_b' : 'pas_pos', 'Strand_b' : 'Strand'}) - - #Distance to polyA site - vcf_apa_df['distance'] = np.abs(vcf_apa_df['Pos'] - vcf_apa_df['pas_pos']) - - #Choose unique SNPs by shortest distance to polyA site (and inverse PIP for tie-breaking) - vcf_apa_df['pip_inv'] = 1. - vcf_apa_df['pip'] - - vcf_apa_df = vcf_apa_df.sort_values(by=['distance', 'pip_inv'], ascending=True).drop_duplicates(subset=['Chromosome', 'Pos', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df.sort_values(['Chromosome', 'Pos', 'alt'], ascending=True).copy().reset_index(drop=True) - - vcf_df_filtered = vcf_apa_df.rename(columns={'Chromosome' : 'chrom', 'Pos' : 'pos', 'Strand' : 'strand'}) - vcf_df_filtered = vcf_df_filtered[['chrom', 'pos', 'ref', 'alt', 'gene_id', 'pas_id', 'strand', 'pas_pos', 'distance', 'variant', 'pip', 'molecular_trait_id']] - - print("len(vcf_df_filtered) = " + str(len(vcf_df_filtered))) - - #Store intermediate SNPs (filtered) - vcf_df_filtered.to_csv("txrev/GTEx_snps_" + tissue_name + "_intronic_polya_finemapped_filtered.bed.gz", sep='\t', index=False) - - #Reload filtered SNP file - vcf_df_filtered = pd.read_csv("txrev/GTEx_snps_" + tissue_name + "_intronic_polya_finemapped_filtered.bed.gz", sep='\t', compression='gzip') - - #Only keep SNPs with PIP > cutoff - pos_df = vcf_df_filtered.query("pip > " + str(pip_cutoff)).copy().reset_index(drop=True) - - #Store final table of positive SNPs - pos_df.to_csv("txrev/GTEx_snps_" + tissue_name + "_intronic_polya_positives.bed.gz", sep='\t', index=False) - - print("len(pos_df) = " + str(len(pos_df))) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/ipaqtl_vcfs.py b/src/scripts/data/qtl_data/ipaqtl_vcfs.py deleted file mode 100644 index 773c45e..0000000 --- a/src/scripts/data/qtl_data/ipaqtl_vcfs.py +++ /dev/null @@ -1,234 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser -import os -import pdb -import time - -import numpy as np -import pandas as pd -import pyranges as pr -from tqdm import tqdm - -''' -ipaqtl_vcfs.py - -Generate positive and negative intronic paQTL sets from the QTL catalog txrevise. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options]' - parser = OptionParser(usage) - parser.add_option('--neg_pip', dest='neg_pip', - default=0.01, type='float', - help='PIP upper limit for negative examples. [Default: %default]') - parser.add_option('--pos_pip', dest='pos_pip', - default=0.9, type='float', - help='PIP lower limit for positive examples. [Default: %default]') - parser.add_option('--match_gene', dest='match_gene', - default=0, type='int', - help='Try finding negative in same gene as positive. [Default: %default]') - parser.add_option('--match_allele', dest='match_allele', - default=0, type='int', - help='Try finding negative with same ref and alt alleles. [Default: %default]') - parser.add_option('-o', dest='out_prefix', - default='qtlcat_ipaqtl') - (options,args) = parser.parse_args() - - tissue_name = options.out_prefix.split('txrev_')[1] - - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort_protein.gtf' - - # read variant table - qtlcat_df_neg = pd.read_csv("ge/GTEx_snps_" + tissue_name + "_intronic_polya_negatives.bed.gz", sep='\t') - qtlcat_df_pos = pd.read_csv("txrev/GTEx_snps_" + tissue_name + "_intronic_polya_positives.bed.gz", sep='\t') - - # read TPM bin table and construct lookup dictionaries - tpm_df = pd.read_csv('ge/GTEx_ge_' + tissue_name + "_tpms.csv", sep='\t')[['gene_id', 'tpm', 'bin_index', 'bin_index_l', 'bin_index_r']] - gene_to_tpm_dict = tpm_df.set_index('gene_id').to_dict(orient='index') - - # filter on SNPs with genes in TPM bin dict - qtlcat_df_neg = qtlcat_df_neg.loc[qtlcat_df_neg['gene_id'].isin(tpm_df['gene_id'].values.tolist())].copy().reset_index(drop=True) - qtlcat_df_pos = qtlcat_df_pos.loc[qtlcat_df_pos['gene_id'].isin(tpm_df['gene_id'].values.tolist())].copy().reset_index(drop=True) - - #Load gene span annotation (protein-coding/categorized only) - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['id_str']) - gtf_genes = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]).unique().tolist() - - # filter on SNPs with genes in GTF file - qtlcat_df_neg = qtlcat_df_neg.loc[qtlcat_df_neg['gene_id'].isin(gtf_genes)].copy().reset_index(drop=True) - qtlcat_df_pos = qtlcat_df_pos.loc[qtlcat_df_pos['gene_id'].isin(gtf_genes)].copy().reset_index(drop=True) - - bin_to_genes_dict = {} - for _, row in tpm_df.iterrows() : - - if row['bin_index'] not in bin_to_genes_dict : - bin_to_genes_dict[row['bin_index']] = [] - - bin_to_genes_dict[row['bin_index']].append(row['gene_id']) - - for sample_bin in bin_to_genes_dict : - bin_to_genes_dict[sample_bin] = set(bin_to_genes_dict[sample_bin]) - - # split molecular trait id and filter for polyadenylation (for positives) - qtlcat_df_pos['gene'] = [mti.split('.')[0] for mti in qtlcat_df_pos.molecular_trait_id] - qtlcat_df_pos['event'] = [mti.split('.')[2] for mti in qtlcat_df_pos.molecular_trait_id] - - qtlcat_df_pos = qtlcat_df_pos[qtlcat_df_pos.event == 'downstream'] - qtlcat_df_pos = qtlcat_df_pos.rename(columns={'distance' : 'pas_dist'}) - - qtlcat_df_neg['molecular_trait_id'] = qtlcat_df_neg['gene_id'] + "." + "grp_0.downstream.negative" - qtlcat_df_neg['gene'] = qtlcat_df_neg['gene_id'] - qtlcat_df_neg['event'] = 'downstream' - qtlcat_df_neg = qtlcat_df_neg.rename(columns={'distance' : 'pas_dist'}) - - paqtl_df = pd.concat([qtlcat_df_neg, qtlcat_df_pos]).copy().reset_index(drop=True) - - # determine positive variants - paqtl_pos_df = paqtl_df[paqtl_df.pip >= options.pos_pip] - paqtl_neg_df = paqtl_df[paqtl_df.pip < options.neg_pip] - pos_variants = set(paqtl_pos_df.variant) - - neg_gene_and_allele_variants = 0 - neg_gene_variants = 0 - - neg_expr_and_allele_variants = 0 - neg_expr_variants = 0 - - unmatched_variants = 0 - - # choose negative variants - neg_variants = set() - neg_dict = {} - for pvariant in tqdm(pos_variants): - paqtl_this_df = paqtl_pos_df[paqtl_pos_df.variant == pvariant] - - neg_found = False - - # optionally prefer negative from positive's gene set - if options.match_gene == 1 and options.match_allele == 1 : - pgenes = set(paqtl_this_df.gene) - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if neg_found : - neg_gene_and_allele_variants += 1 - - if not neg_found and options.match_gene == 1 : - pgenes = set(paqtl_this_df.gene) - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if neg_found : - neg_gene_variants += 1 - - if not neg_found and options.match_allele == 1 : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if neg_found : - neg_expr_and_allele_variants += 1 - - if not neg_found : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if neg_found : - neg_expr_variants += 1 - - if not neg_found : - print("[Warning] Could not find a matching negative for '" + pvariant + "'") - unmatched_variants += 1 - - print('%d positive variants' % len(pos_variants)) - print('%d negative variants' % len(neg_variants)) - print(' - %d gene-matched negatives with same alleles' % neg_gene_and_allele_variants) - print(' - %d gene-matched negatives ' % neg_gene_variants) - print(' - %d expr-matched negatives with same alleles' % neg_expr_and_allele_variants) - print(' - %d expr-matched negatives ' % neg_expr_variants) - print(' - %d unmatched negatives ' % unmatched_variants) - - pos_dict = {pv: pv for pv in pos_variants} - - # write VCFs - write_vcf('%s_pos.vcf' % options.out_prefix, paqtl_df, pos_variants, pos_dict) - write_vcf('%s_neg.vcf' % options.out_prefix, paqtl_df, neg_variants, neg_dict) - -def find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, match_allele) : - - gene_mask = np.array([gene in pgenes for gene in paqtl_neg_df.gene]) - paqtl_neg_gene_df = paqtl_neg_df[gene_mask] - - # match PAS distance - this_dist = paqtl_this_df.iloc[0].pas_dist - dist_cmp = np.abs(paqtl_neg_gene_df.pas_dist - this_dist) - dist_cmp_unique = np.sort(np.unique(dist_cmp.values)) - - this_ref = paqtl_this_df.iloc[0].ref - this_alt = paqtl_this_df.iloc[0].alt - - for ni_unique in dist_cmp_unique: - - paqtl_neg_gene_dist_df = paqtl_neg_gene_df.loc[dist_cmp == ni_unique] - - shuffle_index = np.arange(len(paqtl_neg_gene_dist_df), dtype='int32') - np.random.shuffle(shuffle_index) - - for npaqtl_i in range(len(paqtl_neg_gene_dist_df)) : - npaqtl = paqtl_neg_gene_dist_df.iloc[shuffle_index[npaqtl_i]] - - if not match_allele or (npaqtl.ref == this_ref and npaqtl.alt == this_alt): - if npaqtl.variant not in neg_variants and npaqtl.variant not in pos_variants: - - neg_variants.add(npaqtl.variant) - neg_dict[npaqtl.variant] = paqtl_this_df.iloc[0].variant - - return True - - return False - -def write_vcf(vcf_file, df, variants_write, variants_dict): - vcf_open = open(vcf_file, 'w') - print('##fileformat=VCFv4.2', file=vcf_open) - print('##INFO=', - file=vcf_open) - print('##INFO=', - file=vcf_open) - print('##INFO=', - file=vcf_open) - cols = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] - print('\t'.join(cols), file=vcf_open) - - variants_written = set() - - for v in df.itertuples(): - if v.variant in variants_write and v.variant not in variants_written: - cols = [v.chrom, str(v.pos), v.variant, v.ref, v.alt, '.', '.'] - cols += ['MT=%s;PD=%d;PI=%s' % (v.molecular_trait_id, v.pas_dist, variants_dict[v.variant])] - print('\t'.join(cols), file=vcf_open) - variants_written.add(v.variant) - - vcf_open.close() - - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/make_expression_tables.py b/src/scripts/data/qtl_data/make_expression_tables.py deleted file mode 100644 index ddc2a63..0000000 --- a/src/scripts/data/qtl_data/make_expression_tables.py +++ /dev/null @@ -1,181 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -import pyranges as pr - -import matplotlib.pyplot as plt - -''' -make_expression_tables.py - -Contruct TPM bucket to sample genes from. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Define tissue column-to-file mapping - tissue_dict = { - 'Adipose - Subcutaneous' : 'adipose_subcutaneous', - 'Adipose - Visceral (Omentum)' : 'adipose_visceral', - 'Adrenal Gland' : 'adrenal_gland', - 'Artery - Aorta' : 'artery_aorta', - 'Artery - Coronary' : 'artery_coronary', - 'Artery - Tibial' : 'artery_tibial', - 'Whole Blood' : 'blood', - 'Brain - Amygdala' : 'brain_amygdala', - 'Brain - Anterior cingulate cortex (BA24)' : 'brain_anterior_cingulate_cortex', - 'Brain - Caudate (basal ganglia)' : 'brain_caudate', - 'Brain - Cerebellar Hemisphere' : 'brain_cerebellar_hemisphere', - 'Brain - Cerebellum' : 'brain_cerebellum', - 'Brain - Cortex' : 'brain_cortex', - 'Brain - Frontal Cortex (BA9)' : 'brain_frontal_cortex', - 'Brain - Hippocampus' : 'brain_hippocampus', - 'Brain - Hypothalamus' : 'brain_hypothalamus', - 'Brain - Nucleus accumbens (basal ganglia)' : 'brain_nucleus_accumbens', - 'Brain - Putamen (basal ganglia)' : 'brain_putamen', - 'Brain - Spinal cord (cervical c-1)' : 'brain_spinal_cord', - 'Brain - Substantia nigra' : 'brain_substantia_nigra', - 'Breast - Mammary Tissue' : 'breast', - 'Colon - Sigmoid' : 'colon_sigmoid', - 'Colon - Transverse' : 'colon_transverse', - 'Esophagus - Gastroesophageal Junction' : 'esophagus_gej', - 'Esophagus - Mucosa' : 'esophagus_mucosa', - 'Esophagus - Muscularis' : 'esophagus_muscularis', - 'Cells - Cultured fibroblasts' : 'fibroblast', - 'Heart - Atrial Appendage' : 'heart_atrial_appendage', - 'Heart - Left Ventricle' : 'heart_left_ventricle', - 'Kidney - Cortex' : 'kidney_cortex', - 'Cells - EBV-transformed lymphocytes' : 'LCL', - 'Liver' : 'liver', - 'Lung' : 'lung', - 'Minor Salivary Gland' : 'minor_salivary_gland', - 'Muscle - Skeletal' : 'muscle', - 'Nerve - Tibial' : 'nerve_tibial', - 'Ovary' : 'ovary', - 'Pancreas' : 'pancreas', - 'Pituitary' : 'pituitary', - 'Prostate' : 'prostate', - 'Skin - Not Sun Exposed (Suprapubic)' : 'skin_not_sun_exposed', - 'Skin - Sun Exposed (Lower leg)' : 'skin_sun_exposed', - 'Small Intestine - Terminal Ileum' : 'small_intestine', - 'Spleen' : 'spleen', - 'Stomach' : 'stomach', - 'Testis' : 'testis', - 'Thyroid' : 'thyroid', - 'Uterus' : 'uterus', - 'Vagina' : 'vagina', - } - - for tissue_name in tissue_dict : - - #Load TPM matrix - tpm_df = pd.read_csv("GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz", sep='\t', compression='gzip', skiprows=2) - - save_name = tissue_dict[tissue_name] - - print("-- " + save_name + " --") - - #Clean dataframe - tpm_df['gene_id'] = tpm_df['Name'].apply(lambda x: x.split(".")[0]) - - tpm_df = tpm_df.drop_duplicates(subset=['gene_id'], keep='first').copy().reset_index(drop=True) - - tpm_df['tpm'] = tpm_df[tissue_name] - tpm_df = tpm_df[['gene_id', 'tpm']] - - #Get non-zero TPM entries - tpm_df_zero = tpm_df.loc[tpm_df['tpm'] == 0].copy().reset_index(drop=True) - tpm_df_nonzero = tpm_df.loc[tpm_df['tpm'] > 0].copy().reset_index(drop=True) - - tpm_df_zero['tpm_log2'] = 0. - tpm_df_nonzero['tpm_log2'] = np.log2(tpm_df_nonzero['tpm']) - - #Clip at extremes - min_q = 0.0075 - max_q = 0.9925 - - #Log2 fold change bin sizes - bin_size = 0.4 - bin_offset = 0.15 - - min_tpm_log2 = np.quantile(tpm_df_nonzero['tpm_log2'], q=min_q) - max_tpm_log2 = np.quantile(tpm_df_nonzero['tpm_log2'], q=max_q) - - tpm_df_nonzero.loc[tpm_df_nonzero['tpm_log2'] < min_tpm_log2, 'tpm_log2'] = min_tpm_log2 - tpm_df_nonzero.loc[tpm_df_nonzero['tpm_log2'] > max_tpm_log2, 'tpm_log2'] = max_tpm_log2 - - tpm_log2 = tpm_df_nonzero['tpm_log2'].values - - n_bins = int((max_tpm_log2 - min_tpm_log2) / bin_size) - - #Get sample bins - sample_bins = np.linspace(min_tpm_log2, max_tpm_log2, n_bins+1) - - #Map values to bins - bin_index = np.digitize(tpm_log2, sample_bins[1:], right=True) - bin_index_l = np.digitize(tpm_log2 - bin_offset, sample_bins[1:], right=True) - bin_index_r = np.digitize(tpm_log2 + bin_offset, sample_bins[1:], right=True) - - tpm_df_zero['bin_index_l'] = -1 * np.ones(len(tpm_df_zero), dtype='int32') - tpm_df_zero['bin_index'] = -1 * np.ones(len(tpm_df_zero), dtype='int32') - tpm_df_zero['bin_index_r'] = -1 * np.ones(len(tpm_df_zero), dtype='int32') - - tpm_df_nonzero['bin_index_l'] = bin_index_l - tpm_df_nonzero['bin_index'] = bin_index - tpm_df_nonzero['bin_index_r'] = bin_index_r - - tpm_df = pd.concat([tpm_df_zero, tpm_df_nonzero]).copy().reset_index(drop=True) - - tpm_df = tpm_df.sort_values(by='gene_id', ascending=True).copy().reset_index(drop=True) - - #Save dataframe - tpm_df.to_csv('ge/GTEx_ge_' + save_name + "_tpms.csv", sep='\t', index=False) - - #Visualize TPM sample bins - tpm_df_filtered = tpm_df.loc[tpm_df['tpm'] > 0.] - - f = plt.figure(figsize=(4, 3)) - - plt.hist(tpm_df_filtered['bin_index'].values, bins=np.unique(tpm_df_filtered['bin_index'].values)) - - plt.xlim(0, np.max(tpm_df_filtered['bin_index'].values)) - - plt.xticks(fontsize=8) - plt.yticks(fontsize=8) - - plt.xlabel("Sample bin (FC < " + str(round(2**(bin_size+2*bin_offset), 2)) + ")", fontsize=8) - plt.ylabel("# of genes", fontsize=8) - - plt.title("TPM sample bins (" + save_name + ")", fontsize=8) - - plt.tight_layout() - - plt.savefig('ge/GTEx_ge_' + save_name + "_tpms.png", transparent=False, dpi=300) - - plt.close() - - #Check and warn in case of low-support bins - _, bin_support = np.unique(tpm_df_filtered['bin_index'].values, return_counts=True) - - if np.any(bin_support < 100) : - print("[Warning] Less than 100 genes in some of the TPM sample bins (min = " + str(int(np.min(bin_support))) + ").") - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/make_vcfs.py b/src/scripts/data/qtl_data/make_vcfs.py deleted file mode 100644 index aa251d0..0000000 --- a/src/scripts/data/qtl_data/make_vcfs.py +++ /dev/null @@ -1,112 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import glob -import os - -import pandas as pd - -import util - -''' -make_vcfs.py - -Download QTL Catalogue fine-mapping results. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - pip = 0.2 - match_gene = 0 - match_allele = 1 - - ################################################ - # intronic polyA QTLs - - out_dir = 'ipaqtl_pip%d%s%s' % (pip*100, 'g' if match_gene == 1 else 'e', 'a' if match_allele else '') - os.makedirs(out_dir, exist_ok=True) - - jobs = [] - for table_file in glob.glob('txrev/*.txt.gz'): - out_prefix = table_file.replace('txrev/', '%s/' % out_dir) - out_prefix = out_prefix.replace('.purity_filtered.txt.gz', '') - cmd = './ipaqtl_vcfs.py --neg_pip 0.01 --pos_pip %f --match_gene %d --match_allele %d -o %s' % (pip, match_gene, match_allele, out_prefix) - jobs.append(cmd) - util.exec_par(jobs, 6, verbose=True) - - # merge study/tissue variants - mpos_vcf_file = '%s/pos_merge.vcf' % out_dir - mneg_vcf_file = '%s/neg_merge.vcf' % out_dir - merge_variants(mpos_vcf_file, '%s/*_pos.vcf' % out_dir) - merge_variants(mneg_vcf_file, '%s/*_neg.vcf' % out_dir) - - - ################################################ - # polyA QTLs - - out_dir = 'paqtl_pip%d%s%s' % (pip*100, 'g' if match_gene == 1 else 'e', 'a' if match_allele else '') - os.makedirs(out_dir, exist_ok=True) - - jobs = [] - for table_file in glob.glob('txrev/*.txt.gz'): - out_prefix = table_file.replace('txrev/', '%s/' % out_dir) - out_prefix = out_prefix.replace('.purity_filtered.txt.gz', '') - cmd = './paqtl_vcfs.py --neg_pip 0.01 --pos_pip %f --match_gene %d --match_allele %d -o %s' % (pip, match_gene, match_allele, out_prefix) - jobs.append(cmd) - util.exec_par(jobs, 6, verbose=True) - - # merge study/tissue variants - mpos_vcf_file = '%s/pos_merge.vcf' % out_dir - mneg_vcf_file = '%s/neg_merge.vcf' % out_dir - merge_variants(mpos_vcf_file, '%s/*_pos.vcf' % out_dir) - merge_variants(mneg_vcf_file, '%s/*_neg.vcf' % out_dir) - - ################################################ - # splicing QTLs - - out_dir = 'sqtl_pip%d%s%s' % (pip*100, 'g' if match_gene == 1 else 'e', 'a' if match_allele else '') - os.makedirs(out_dir, exist_ok=True) - - jobs = [] - for table_file in glob.glob('txrev/*.txt.gz'): - out_prefix = table_file.replace('txrev/', '%s/' % out_dir) - out_prefix = out_prefix.replace('.purity_filtered.txt.gz', '') - cmd = './sqtl_vcfs.py --neg_pip 0.01 --pos_pip %f --match_gene %d --match_allele %d -o %s' % (pip, match_gene, match_allele, out_prefix) - jobs.append(cmd) - util.exec_par(jobs, 6, verbose=True) - - # merge study/tissue variants - mpos_vcf_file = '%s/pos_merge.vcf' % out_dir - mneg_vcf_file = '%s/neg_merge.vcf' % out_dir - merge_variants(mpos_vcf_file, '%s/*_pos.vcf' % out_dir) - merge_variants(mneg_vcf_file, '%s/*_neg.vcf' % out_dir) - - -def merge_variants(merge_vcf_file, vcf_glob): - with open(merge_vcf_file, 'w') as merge_vcf_open: - vcf0_file = list(glob.glob(vcf_glob))[0] - for line in open(vcf0_file): - if line[0] == '#': - print(line, end='', file=merge_vcf_open) - - merged_variants = set() - for vcf_file in glob.glob(vcf_glob): - for line in open(vcf_file): - if not line.startswith('#'): - variant = line.split()[2] - if variant not in merged_variants: - print(line, file=merge_vcf_open, end='') - merged_variants.add(variant) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/merge_finemapping_tables.py b/src/scripts/data/qtl_data/merge_finemapping_tables.py deleted file mode 100644 index ac4fa7d..0000000 --- a/src/scripts/data/qtl_data/merge_finemapping_tables.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -''' -merge_finemapping_tables.py - -Merge fine-mapping tables of QTL credible sets. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Define tissues - tissue_names = [ - 'adipose_subcutaneous', - 'adipose_visceral', - 'adrenal_gland', - 'artery_aorta', - 'artery_coronary', - 'artery_tibial', - 'blood', - 'brain_amygdala', - 'brain_anterior_cingulate_cortex', - 'brain_caudate', - 'brain_cerebellar_hemisphere', - 'brain_cerebellum', - 'brain_cortex', - 'brain_frontal_cortex', - 'brain_hippocampus', - 'brain_hypothalamus', - 'brain_nucleus_accumbens', - 'brain_putamen', - 'brain_spinal_cord', - 'brain_substantia_nigra', - 'breast', - 'colon_sigmoid', - 'colon_transverse', - 'esophagus_gej', - 'esophagus_mucosa', - 'esophagus_muscularis', - 'fibroblast', - 'heart_atrial_appendage', - 'heart_left_ventricle', - 'kidney_cortex', - 'LCL', - 'liver', - 'lung', - 'minor_salivary_gland', - 'muscle', - 'nerve_tibial', - 'ovary', - 'pancreas', - 'pituitary', - 'prostate', - 'skin_not_sun_exposed', - 'skin_sun_exposed', - 'small_intestine', - 'spleen', - 'stomach', - 'testis', - 'thyroid', - 'uterus', - 'vagina', - ] - - #Load and merge fine-mapping results - dfs = [] - for tissue_name in tissue_names : - - print("-- " + tissue_name + " --") - - df = pd.read_csv("txrev/GTEx_txrev_" + tissue_name + ".purity_filtered.txt.gz", sep='\t', usecols=['chromosome', 'position', 'ref', 'alt', 'variant', 'pip'], low_memory=False) - dfs.append(df.sort_values(by='pip', ascending=False).drop_duplicates(subset=['variant'], keep='first').copy().reset_index(drop=True)) - - df = pd.concat(dfs).sort_values(by='pip', ascending=False).drop_duplicates(subset=['variant'], keep='first').copy().reset_index(drop=True) - - df['chromosome'] = "chr" + df['chromosome'].astype(str) - df = df.rename(columns={'chromosome' : 'chrom', 'position' : 'pos'}) - - print("len(df) = " + str(len(df))) - - #Save union of dataframes - df.to_csv("txrev/GTEx_txrev_finemapped_merged.csv.gz", sep='\t', index=False) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/paqtl_make_negative_sets.py b/src/scripts/data/qtl_data/paqtl_make_negative_sets.py deleted file mode 100644 index a5da60d..0000000 --- a/src/scripts/data/qtl_data/paqtl_make_negative_sets.py +++ /dev/null @@ -1,196 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -import pyranges as pr - -''' -paqtl_make_negative_sets.py - -Build tables with negative (non-causal) SNPs for paQTLs. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Parameters - pip_cutoff = 0.01 - max_distance = 10000 - gene_pad = 50 - apa_file = '/home/drk/common/data/genomes/hg38/genes/polyadb/polyadb_exon3.bed' - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort.gtf' - finemap_file = 'txrev/GTEx_txrev_finemapped_merged.csv.gz' - - #Define tissues - tissue_names = [ - 'adipose_subcutaneous', - 'adipose_visceral', - 'adrenal_gland', - 'artery_aorta', - 'artery_coronary', - 'artery_tibial', - 'blood', - 'brain_amygdala', - 'brain_anterior_cingulate_cortex', - 'brain_caudate', - 'brain_cerebellar_hemisphere', - 'brain_cerebellum', - 'brain_cortex', - 'brain_frontal_cortex', - 'brain_hippocampus', - 'brain_hypothalamus', - 'brain_nucleus_accumbens', - 'brain_putamen', - 'brain_spinal_cord', - 'brain_substantia_nigra', - 'breast', - 'colon_sigmoid', - 'colon_transverse', - 'esophagus_gej', - 'esophagus_mucosa', - 'esophagus_muscularis', - 'fibroblast', - 'heart_atrial_appendage', - 'heart_left_ventricle', - 'kidney_cortex', - 'LCL', - 'liver', - 'lung', - 'minor_salivary_gland', - 'muscle', - 'nerve_tibial', - 'ovary', - 'pancreas', - 'pituitary', - 'prostate', - 'skin_not_sun_exposed', - 'skin_sun_exposed', - 'small_intestine', - 'spleen', - 'stomach', - 'testis', - 'thyroid', - 'uterus', - 'vagina', - ] - - #Compile negative SNP set for each tissue - for tissue_name in tissue_names : - - print("-- " + str(tissue_name) + " --") - - #Load summary stats and extract unique set of SNPs - vcf_df = pd.read_csv("ge/GTEx_ge_" + tissue_name + ".all.tsv.gz", sep='\t', compression='gzip', usecols=['chromosome', 'position', 'ref', 'alt']).drop_duplicates(subset=['chromosome', 'position', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - - #Only keep SNPs (no indels) - vcf_df = vcf_df.loc[(vcf_df['ref'].str.len() == vcf_df['alt'].str.len()) & (vcf_df['ref'].str.len() == 1)].copy().reset_index(drop=True) - - vcf_df['chromosome'] = 'chr' + vcf_df['chromosome'].astype(str) - vcf_df['start'] = vcf_df['position'].astype(int) - vcf_df['end'] = vcf_df['start'] + 1 - vcf_df['strand'] = "." - - vcf_df = vcf_df[['chromosome', 'start', 'end', 'ref', 'alt', 'strand']] - vcf_df = vcf_df.rename(columns={'chromosome' : 'Chromosome', 'start' : 'Start', 'end' : 'End', 'strand' : 'Strand'}) - - print("len(vcf_df) = " + str(len(vcf_df))) - - #Store intermediate SNPs - #vcf_df.to_csv("ge/GTEx_snps_" + tissue_name + ".bed.gz", sep='\t', index=False, header=False) - - #Load polyadenylation site annotation - apa_df = pd.read_csv(apa_file, sep='\t', names=['Chromosome', 'Start', 'End', 'pas_id', 'feat1', 'Strand']) - apa_df['Start'] += 1 - - #Load gene span annotation - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str']) - gtf_df = gtf_df.query("feature == 'gene'").copy().reset_index(drop=True) - - gtf_df['gene_id'] = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]) - - gtf_df = gtf_df[['Chromosome', 'Start', 'End', 'gene_id', 'feat1', 'Strand']].drop_duplicates(subset=['gene_id'], keep='first').copy().reset_index(drop=True) - - gtf_df['Start'] = gtf_df['Start'].astype(int) - gene_pad - gtf_df['End'] = gtf_df['End'].astype(int) + gene_pad - - #Join dataframes against gtf annotation - apa_pr = pr.PyRanges(apa_df) - gtf_pr = pr.PyRanges(gtf_df) - vcf_pr = pr.PyRanges(vcf_df) - - apa_gtf_pr = apa_pr.join(gtf_pr, strandedness='same') - vcf_gtf_pr = vcf_pr.join(gtf_pr, strandedness=False) - - apa_gtf_df = apa_gtf_pr.df[['Chromosome', 'Start', 'End', 'pas_id', 'gene_id', 'Strand']].copy().reset_index(drop=True) - vcf_gtf_df = vcf_gtf_pr.df[['Chromosome', 'Start', 'End', 'ref', 'alt', 'Strand', 'gene_id']].copy().reset_index(drop=True) - - apa_gtf_df['Start'] -= max_distance - apa_gtf_df['End'] += max_distance - - #Join vcf against polyadenylation annotation - apa_gtf_pr = pr.PyRanges(apa_gtf_df) - vcf_gtf_pr = pr.PyRanges(vcf_gtf_df) - - vcf_apa_pr = vcf_gtf_pr.join(apa_gtf_pr, strandedness=False) - - #Force gene_id of SNP to be same as the gene_id of the polyA site - vcf_apa_df = vcf_apa_pr.df.query("gene_id == gene_id_b").copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df[['Chromosome', 'Start', 'ref', 'alt', 'gene_id', 'pas_id', 'Strand_b', 'Start_b']] - - #PolyA site position - vcf_apa_df['Start_b'] += max_distance - vcf_apa_df = vcf_apa_df.rename(columns={'Start' : 'Pos', 'Start_b' : 'pas_pos', 'Strand_b' : 'Strand'}) - - #Distance to polyA site - vcf_apa_df['distance'] = np.abs(vcf_apa_df['Pos'] - vcf_apa_df['pas_pos']) - - #Choose unique SNPs by shortest distance to polyA site - vcf_apa_df = vcf_apa_df.sort_values(by='distance', ascending=True).drop_duplicates(subset=['Chromosome', 'Pos', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df.sort_values(['Chromosome', 'Pos', 'alt'], ascending=True).copy().reset_index(drop=True) - - vcf_df_filtered = vcf_apa_df.rename(columns={'Chromosome' : 'chrom', 'Pos' : 'pos', 'Strand' : 'strand'}) - vcf_df_filtered = vcf_df_filtered[['chrom', 'pos', 'ref', 'alt', 'gene_id', 'pas_id', 'strand', 'pas_pos', 'distance']] - - print("len(vcf_df_filtered) = " + str(len(vcf_df_filtered))) - - #Store intermediate SNPs (filtered) - vcf_df_filtered.to_csv("ge/GTEx_snps_" + tissue_name + "_polya_filtered.bed.gz", sep='\t', index=False) - - #Reload filtered SNP file - vcf_df_filtered = pd.read_csv("ge/GTEx_snps_" + tissue_name + "_polya_filtered.bed.gz", sep='\t', compression='gzip') - - #Create variant identifier - vcf_df_filtered['variant'] = vcf_df_filtered['chrom'] + "_" + vcf_df_filtered['pos'].astype(str) + "_" + vcf_df_filtered['ref'] + "_" + vcf_df_filtered['alt'] - - #Load merged fine-mapping dataframe - finemap_df = pd.read_csv(finemap_file, sep='\t')[['variant', 'pip']] - - #Join against fine-mapping dataframe - neg_df = vcf_df_filtered.join(finemap_df.set_index('variant'), on='variant', how='left') - neg_df.loc[neg_df['pip'].isnull(), 'pip'] = 0. - - #Only keep SNPs with PIP < cutoff - neg_df = neg_df.query("pip < " + str(pip_cutoff)).copy().reset_index(drop=True) - - #Store final table of negative SNPs - neg_df.to_csv("ge/GTEx_snps_" + tissue_name + "_polya_negatives.bed.gz", sep='\t', index=False) - - print("len(neg_df) = " + str(len(neg_df))) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/paqtl_make_positive_sets.py b/src/scripts/data/qtl_data/paqtl_make_positive_sets.py deleted file mode 100644 index 3d07fa3..0000000 --- a/src/scripts/data/qtl_data/paqtl_make_positive_sets.py +++ /dev/null @@ -1,191 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -import pyranges as pr - -''' -paqtl_make_positive_sets.py - -Build tables with positive (causal) SNPs for paQTLs. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Parameters - pip_cutoff = 0.01 - max_distance = 10000 - gene_pad = 50 - apa_file = '/home/drk/common/data/genomes/hg38/genes/polyadb/polyadb_exon3.bed' - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort.gtf' - - #Define tissues - tissue_names = [ - 'adipose_subcutaneous', - 'adipose_visceral', - 'adrenal_gland', - 'artery_aorta', - 'artery_coronary', - 'artery_tibial', - 'blood', - 'brain_amygdala', - 'brain_anterior_cingulate_cortex', - 'brain_caudate', - 'brain_cerebellar_hemisphere', - 'brain_cerebellum', - 'brain_cortex', - 'brain_frontal_cortex', - 'brain_hippocampus', - 'brain_hypothalamus', - 'brain_nucleus_accumbens', - 'brain_putamen', - 'brain_spinal_cord', - 'brain_substantia_nigra', - 'breast', - 'colon_sigmoid', - 'colon_transverse', - 'esophagus_gej', - 'esophagus_mucosa', - 'esophagus_muscularis', - 'fibroblast', - 'heart_atrial_appendage', - 'heart_left_ventricle', - 'kidney_cortex', - 'LCL', - 'liver', - 'lung', - 'minor_salivary_gland', - 'muscle', - 'nerve_tibial', - 'ovary', - 'pancreas', - 'pituitary', - 'prostate', - 'skin_not_sun_exposed', - 'skin_sun_exposed', - 'small_intestine', - 'spleen', - 'stomach', - 'testis', - 'thyroid', - 'uterus', - 'vagina', - ] - - #Compile positive SNP set for each tissue - for tissue_name in tissue_names : - - print("-- " + str(tissue_name) + " --") - - #Load fine-mapping table - vcf_df = pd.read_csv("txrev/GTEx_txrev_" + tissue_name + ".purity_filtered.txt.gz", sep='\t', usecols=['chromosome', 'position', 'ref', 'alt', 'variant', 'pip', 'molecular_trait_id'], low_memory=False) - - #Only keep SNPs (no indels) - vcf_df = vcf_df.loc[(vcf_df['ref'].str.len() == vcf_df['alt'].str.len()) & (vcf_df['ref'].str.len() == 1)].copy().reset_index(drop=True) - - #Only keep SNPs associated with polyadenylation events - vcf_df = vcf_df.loc[vcf_df['molecular_trait_id'].str.contains(".downstream.")].copy().reset_index(drop=True) - - vcf_df['chromosome'] = 'chr' + vcf_df['chromosome'].astype(str) - vcf_df['start'] = vcf_df['position'].astype(int) - vcf_df['end'] = vcf_df['start'] + 1 - vcf_df['strand'] = "." - - vcf_df = vcf_df[['chromosome', 'start', 'end', 'ref', 'alt', 'strand', 'variant', 'pip', 'molecular_trait_id']] - vcf_df = vcf_df.rename(columns={'chromosome' : 'Chromosome', 'start' : 'Start', 'end' : 'End', 'strand' : 'Strand'}) - - print("len(vcf_df) = " + str(len(vcf_df))) - - #Load polyadenylation site annotation - apa_df = pd.read_csv(apa_file, sep='\t', names=['Chromosome', 'Start', 'End', 'pas_id', 'feat1', 'Strand']) - apa_df['Start'] += 1 - - #Load gene span annotation - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str']) - gtf_df = gtf_df.query("feature == 'gene'").copy().reset_index(drop=True) - - gtf_df['gene_id'] = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]) - - gtf_df = gtf_df[['Chromosome', 'Start', 'End', 'gene_id', 'feat1', 'Strand']].drop_duplicates(subset=['gene_id'], keep='first').copy().reset_index(drop=True) - - gtf_df['Start'] = gtf_df['Start'].astype(int) - gene_pad - gtf_df['End'] = gtf_df['End'].astype(int) + gene_pad - - #Join dataframes against gtf annotation - apa_pr = pr.PyRanges(apa_df) - gtf_pr = pr.PyRanges(gtf_df) - vcf_pr = pr.PyRanges(vcf_df) - - apa_gtf_pr = apa_pr.join(gtf_pr, strandedness='same') - vcf_gtf_pr = vcf_pr.join(gtf_pr, strandedness=False) - - apa_gtf_df = apa_gtf_pr.df[['Chromosome', 'Start', 'End', 'pas_id', 'gene_id', 'Strand']].copy().reset_index(drop=True) - vcf_gtf_df = vcf_gtf_pr.df[['Chromosome', 'Start', 'End', 'ref', 'alt', 'Strand', 'gene_id', 'variant', 'pip', 'molecular_trait_id']].copy().reset_index(drop=True) - - apa_gtf_df['Start'] -= max_distance - apa_gtf_df['End'] += max_distance - - #Join vcf against polyadenylation annotation - apa_gtf_pr = pr.PyRanges(apa_gtf_df) - vcf_gtf_pr = pr.PyRanges(vcf_gtf_df) - - vcf_apa_pr = vcf_gtf_pr.join(apa_gtf_pr, strandedness=False) - - #Force gene_id of SNP to be same as the gene_id of the polyA site - vcf_apa_df = vcf_apa_pr.df.query("gene_id == gene_id_b").copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df[['Chromosome', 'Start', 'ref', 'alt', 'gene_id', 'pas_id', 'Strand_b', 'Start_b', 'variant', 'pip', 'molecular_trait_id']] - - #Force gene_id of SNP to be same as the gene_id of the finemapped molecular trait - vcf_apa_df['molecular_trait_gene_id'] = vcf_apa_df['molecular_trait_id'].apply(lambda x: x.split(".")[0]) - vcf_apa_df = vcf_apa_df.query("gene_id == molecular_trait_gene_id").copy().reset_index(drop=True) - - #PolyA site position - vcf_apa_df['Start_b'] += max_distance - vcf_apa_df = vcf_apa_df.rename(columns={'Start' : 'Pos', 'Start_b' : 'pas_pos', 'Strand_b' : 'Strand'}) - - #Distance to polyA site - vcf_apa_df['distance'] = np.abs(vcf_apa_df['Pos'] - vcf_apa_df['pas_pos']) - - #Choose unique SNPs by shortest distance to polyA site (and inverse PIP for tie-breaking) - vcf_apa_df['pip_inv'] = 1. - vcf_apa_df['pip'] - - vcf_apa_df = vcf_apa_df.sort_values(by=['distance', 'pip_inv'], ascending=True).drop_duplicates(subset=['Chromosome', 'Pos', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - vcf_apa_df = vcf_apa_df.sort_values(['Chromosome', 'Pos', 'alt'], ascending=True).copy().reset_index(drop=True) - - vcf_df_filtered = vcf_apa_df.rename(columns={'Chromosome' : 'chrom', 'Pos' : 'pos', 'Strand' : 'strand'}) - vcf_df_filtered = vcf_df_filtered[['chrom', 'pos', 'ref', 'alt', 'gene_id', 'pas_id', 'strand', 'pas_pos', 'distance', 'variant', 'pip', 'molecular_trait_id']] - - print("len(vcf_df_filtered) = " + str(len(vcf_df_filtered))) - - #Store intermediate SNPs (filtered) - vcf_df_filtered.to_csv("txrev/GTEx_snps_" + tissue_name + "_polya_finemapped_filtered.bed.gz", sep='\t', index=False) - - #Reload filtered SNP file - vcf_df_filtered = pd.read_csv("txrev/GTEx_snps_" + tissue_name + "_polya_finemapped_filtered.bed.gz", sep='\t', compression='gzip') - - #Only keep SNPs with PIP > cutoff - pos_df = vcf_df_filtered.query("pip > " + str(pip_cutoff)).copy().reset_index(drop=True) - - #Store final table of positive SNPs - pos_df.to_csv("txrev/GTEx_snps_" + tissue_name + "_polya_positives.bed.gz", sep='\t', index=False) - - print("len(pos_df) = " + str(len(pos_df))) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/paqtl_vcfs.py b/src/scripts/data/qtl_data/paqtl_vcfs.py deleted file mode 100644 index f0884b1..0000000 --- a/src/scripts/data/qtl_data/paqtl_vcfs.py +++ /dev/null @@ -1,234 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser -import os -import pdb -import time - -import numpy as np -import pandas as pd -import pyranges as pr -from tqdm import tqdm - -''' -paqtl_vcfs.py - -Generate positive and negative paQTL sets from the QTL catalog txrevise. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options]' - parser = OptionParser(usage) - parser.add_option('--neg_pip', dest='neg_pip', - default=0.01, type='float', - help='PIP upper limit for negative examples. [Default: %default]') - parser.add_option('--pos_pip', dest='pos_pip', - default=0.9, type='float', - help='PIP lower limit for positive examples. [Default: %default]') - parser.add_option('--match_gene', dest='match_gene', - default=0, type='int', - help='Try finding negative in same gene as positive. [Default: %default]') - parser.add_option('--match_allele', dest='match_allele', - default=0, type='int', - help='Try finding negative with same ref and alt alleles. [Default: %default]') - parser.add_option('-o', dest='out_prefix', - default='qtlcat_paqtl') - (options,args) = parser.parse_args() - - tissue_name = options.out_prefix.split('txrev_')[1] - - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort_protein.gtf' - - # read variant table - qtlcat_df_neg = pd.read_csv("ge/GTEx_snps_" + tissue_name + "_polya_negatives.bed.gz", sep='\t') - qtlcat_df_pos = pd.read_csv("txrev/GTEx_snps_" + tissue_name + "_polya_positives.bed.gz", sep='\t') - - # read TPM bin table and construct lookup dictionaries - tpm_df = pd.read_csv('ge/GTEx_ge_' + tissue_name + "_tpms.csv", sep='\t')[['gene_id', 'tpm', 'bin_index', 'bin_index_l', 'bin_index_r']] - gene_to_tpm_dict = tpm_df.set_index('gene_id').to_dict(orient='index') - - # filter on SNPs with genes in TPM bin dict - qtlcat_df_neg = qtlcat_df_neg.loc[qtlcat_df_neg['gene_id'].isin(tpm_df['gene_id'].values.tolist())].copy().reset_index(drop=True) - qtlcat_df_pos = qtlcat_df_pos.loc[qtlcat_df_pos['gene_id'].isin(tpm_df['gene_id'].values.tolist())].copy().reset_index(drop=True) - - #Load gene span annotation (protein-coding/categorized only) - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['id_str']) - gtf_genes = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]).unique().tolist() - - # filter on SNPs with genes in GTF file - qtlcat_df_neg = qtlcat_df_neg.loc[qtlcat_df_neg['gene_id'].isin(gtf_genes)].copy().reset_index(drop=True) - qtlcat_df_pos = qtlcat_df_pos.loc[qtlcat_df_pos['gene_id'].isin(gtf_genes)].copy().reset_index(drop=True) - - bin_to_genes_dict = {} - for _, row in tpm_df.iterrows() : - - if row['bin_index'] not in bin_to_genes_dict : - bin_to_genes_dict[row['bin_index']] = [] - - bin_to_genes_dict[row['bin_index']].append(row['gene_id']) - - for sample_bin in bin_to_genes_dict : - bin_to_genes_dict[sample_bin] = set(bin_to_genes_dict[sample_bin]) - - # split molecular trait id and filter for polyadenylation (for positives) - qtlcat_df_pos['gene'] = [mti.split('.')[0] for mti in qtlcat_df_pos.molecular_trait_id] - qtlcat_df_pos['event'] = [mti.split('.')[2] for mti in qtlcat_df_pos.molecular_trait_id] - - qtlcat_df_pos = qtlcat_df_pos[qtlcat_df_pos.event == 'downstream'] - qtlcat_df_pos = qtlcat_df_pos.rename(columns={'distance' : 'pas_dist'}) - - qtlcat_df_neg['molecular_trait_id'] = qtlcat_df_neg['gene_id'] + "." + "grp_0.downstream.negative" - qtlcat_df_neg['gene'] = qtlcat_df_neg['gene_id'] - qtlcat_df_neg['event'] = 'downstream' - qtlcat_df_neg = qtlcat_df_neg.rename(columns={'distance' : 'pas_dist'}) - - paqtl_df = pd.concat([qtlcat_df_neg, qtlcat_df_pos]).copy().reset_index(drop=True) - - # determine positive variants - paqtl_pos_df = paqtl_df[paqtl_df.pip >= options.pos_pip] - paqtl_neg_df = paqtl_df[paqtl_df.pip < options.neg_pip] - pos_variants = set(paqtl_pos_df.variant) - - neg_gene_and_allele_variants = 0 - neg_gene_variants = 0 - - neg_expr_and_allele_variants = 0 - neg_expr_variants = 0 - - unmatched_variants = 0 - - # choose negative variants - neg_variants = set() - neg_dict = {} - for pvariant in tqdm(pos_variants): - paqtl_this_df = paqtl_pos_df[paqtl_pos_df.variant == pvariant] - - neg_found = False - - # optionally prefer negative from positive's gene set - if options.match_gene == 1 and options.match_allele == 1 : - pgenes = set(paqtl_this_df.gene) - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if neg_found : - neg_gene_and_allele_variants += 1 - - if not neg_found and options.match_gene == 1 : - pgenes = set(paqtl_this_df.gene) - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if neg_found : - neg_gene_variants += 1 - - if not neg_found and options.match_allele == 1 : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, True) - - if neg_found : - neg_expr_and_allele_variants += 1 - - if not neg_found : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_l']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if not neg_found and gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[paqtl_this_df.iloc[0].gene]['bin_index_r']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, False) - - if neg_found : - neg_expr_variants += 1 - - if not neg_found : - print("[Warning] Could not find a matching negative for '" + pvariant + "'") - unmatched_variants += 1 - - print('%d positive variants' % len(pos_variants)) - print('%d negative variants' % len(neg_variants)) - print(' - %d gene-matched negatives with same alleles' % neg_gene_and_allele_variants) - print(' - %d gene-matched negatives ' % neg_gene_variants) - print(' - %d expr-matched negatives with same alleles' % neg_expr_and_allele_variants) - print(' - %d expr-matched negatives ' % neg_expr_variants) - print(' - %d unmatched negatives ' % unmatched_variants) - - pos_dict = {pv: pv for pv in pos_variants} - - # write VCFs - write_vcf('%s_pos.vcf' % options.out_prefix, paqtl_df, pos_variants, pos_dict) - write_vcf('%s_neg.vcf' % options.out_prefix, paqtl_df, neg_variants, neg_dict) - -def find_negative(neg_variants, neg_dict, pos_variants, paqtl_this_df, paqtl_neg_df, pgenes, match_allele) : - - gene_mask = np.array([gene in pgenes for gene in paqtl_neg_df.gene]) - paqtl_neg_gene_df = paqtl_neg_df[gene_mask] - - # match PAS distance - this_dist = paqtl_this_df.iloc[0].pas_dist - dist_cmp = np.abs(paqtl_neg_gene_df.pas_dist - this_dist) - dist_cmp_unique = np.sort(np.unique(dist_cmp.values)) - - this_ref = paqtl_this_df.iloc[0].ref - this_alt = paqtl_this_df.iloc[0].alt - - for ni_unique in dist_cmp_unique: - - paqtl_neg_gene_dist_df = paqtl_neg_gene_df.loc[dist_cmp == ni_unique] - - shuffle_index = np.arange(len(paqtl_neg_gene_dist_df), dtype='int32') - np.random.shuffle(shuffle_index) - - for npaqtl_i in range(len(paqtl_neg_gene_dist_df)) : - npaqtl = paqtl_neg_gene_dist_df.iloc[shuffle_index[npaqtl_i]] - - if not match_allele or (npaqtl.ref == this_ref and npaqtl.alt == this_alt): - if npaqtl.variant not in neg_variants and npaqtl.variant not in pos_variants: - - neg_variants.add(npaqtl.variant) - neg_dict[npaqtl.variant] = paqtl_this_df.iloc[0].variant - - return True - - return False - -def write_vcf(vcf_file, df, variants_write, variants_dict): - vcf_open = open(vcf_file, 'w') - print('##fileformat=VCFv4.2', file=vcf_open) - print('##INFO=', - file=vcf_open) - print('##INFO=', - file=vcf_open) - print('##INFO=', - file=vcf_open) - cols = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] - print('\t'.join(cols), file=vcf_open) - - variants_written = set() - - for v in df.itertuples(): - if v.variant in variants_write and v.variant not in variants_written: - cols = [v.chrom, str(v.pos), v.variant, v.ref, v.alt, '.', '.'] - cols += ['MT=%s;PD=%d;PI=%s' % (v.molecular_trait_id, v.pas_dist, variants_dict[v.variant])] - print('\t'.join(cols), file=vcf_open) - variants_written.add(v.variant) - - vcf_open.close() - - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/sqtl_make_negative_sets.py b/src/scripts/data/qtl_data/sqtl_make_negative_sets.py deleted file mode 100644 index 7518ca4..0000000 --- a/src/scripts/data/qtl_data/sqtl_make_negative_sets.py +++ /dev/null @@ -1,195 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -import pyranges as pr - -''' -sqtl_make_negative_sets.py - -Build tables with negative (non-causal) SNPs for sQTLs. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Parameters - pip_cutoff = 0.01 - max_distance = 10000 - gene_pad = 50 - splice_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_protein_splice.gff' - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort.gtf' - finemap_file = 'txrev/GTEx_txrev_finemapped_merged.csv.gz' - - #Define tissues - tissue_names = [ - 'adipose_subcutaneous', - 'adipose_visceral', - 'adrenal_gland', - 'artery_aorta', - 'artery_coronary', - 'artery_tibial', - 'blood', - 'brain_amygdala', - 'brain_anterior_cingulate_cortex', - 'brain_caudate', - 'brain_cerebellar_hemisphere', - 'brain_cerebellum', - 'brain_cortex', - 'brain_frontal_cortex', - 'brain_hippocampus', - 'brain_hypothalamus', - 'brain_nucleus_accumbens', - 'brain_putamen', - 'brain_spinal_cord', - 'brain_substantia_nigra', - 'breast', - 'colon_sigmoid', - 'colon_transverse', - 'esophagus_gej', - 'esophagus_mucosa', - 'esophagus_muscularis', - 'fibroblast', - 'heart_atrial_appendage', - 'heart_left_ventricle', - 'kidney_cortex', - 'LCL', - 'liver', - 'lung', - 'minor_salivary_gland', - 'muscle', - 'nerve_tibial', - 'ovary', - 'pancreas', - 'pituitary', - 'prostate', - 'skin_not_sun_exposed', - 'skin_sun_exposed', - 'small_intestine', - 'spleen', - 'stomach', - 'testis', - 'thyroid', - 'uterus', - 'vagina', - ] - - #Compile negative SNP set for each tissue - for tissue_name in tissue_names : - - print("-- " + str(tissue_name) + " --") - - #Load summary stats and extract unique set of SNPs - vcf_df = pd.read_csv("ge/GTEx_ge_" + tissue_name + ".all.tsv.gz", sep='\t', compression='gzip', usecols=['chromosome', 'position', 'ref', 'alt']).drop_duplicates(subset=['chromosome', 'position', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - - #Only keep SNPs (no indels) - vcf_df = vcf_df.loc[(vcf_df['ref'].str.len() == vcf_df['alt'].str.len()) & (vcf_df['ref'].str.len() == 1)].copy().reset_index(drop=True) - - vcf_df['chromosome'] = 'chr' + vcf_df['chromosome'].astype(str) - vcf_df['start'] = vcf_df['position'].astype(int) - vcf_df['end'] = vcf_df['start'] + 1 - vcf_df['strand'] = "." - - vcf_df = vcf_df[['chromosome', 'start', 'end', 'ref', 'alt', 'strand']] - vcf_df = vcf_df.rename(columns={'chromosome' : 'Chromosome', 'start' : 'Start', 'end' : 'End', 'strand' : 'Strand'}) - - print("len(vcf_df) = " + str(len(vcf_df))) - - #Store intermediate SNPs - #vcf_df.to_csv("ge/GTEx_snps_" + tissue_name + ".bed.gz", sep='\t', index=False, header=False) - - #Load splice site annotation - splice_df = pd.read_csv(splice_file, sep='\t', names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str'], usecols=['Chromosome', 'Start', 'End', 'feature', 'feat1', 'Strand'])[['Chromosome', 'Start', 'End', 'feature', 'feat1', 'Strand']] - - #Load gene span annotation - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str']) - gtf_df = gtf_df.query("feature == 'gene'").copy().reset_index(drop=True) - - gtf_df['gene_id'] = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]) - - gtf_df = gtf_df[['Chromosome', 'Start', 'End', 'gene_id', 'feat1', 'Strand']].drop_duplicates(subset=['gene_id'], keep='first').copy().reset_index(drop=True) - - gtf_df['Start'] = gtf_df['Start'].astype(int) - gene_pad - gtf_df['End'] = gtf_df['End'].astype(int) + gene_pad - - #Join dataframes against gtf annotation - splice_pr = pr.PyRanges(splice_df) - gtf_pr = pr.PyRanges(gtf_df) - vcf_pr = pr.PyRanges(vcf_df) - - splice_gtf_pr = splice_pr.join(gtf_pr, strandedness='same') - vcf_gtf_pr = vcf_pr.join(gtf_pr, strandedness=False) - - splice_gtf_df = splice_gtf_pr.df[['Chromosome', 'Start', 'End', 'feature', 'gene_id', 'Strand']].copy().reset_index(drop=True) - vcf_gtf_df = vcf_gtf_pr.df[['Chromosome', 'Start', 'End', 'ref', 'alt', 'Strand', 'gene_id']].copy().reset_index(drop=True) - - splice_gtf_df['Start'] -= max_distance - splice_gtf_df['End'] += max_distance - - #Join vcf against splice annotation - splice_gtf_pr = pr.PyRanges(splice_gtf_df) - vcf_gtf_pr = pr.PyRanges(vcf_gtf_df) - - vcf_splice_pr = vcf_gtf_pr.join(splice_gtf_pr, strandedness=False) - - #Force gene_id of SNP to be same as the gene_id of the splice site - vcf_splice_df = vcf_splice_pr.df.query("gene_id == gene_id_b").copy().reset_index(drop=True) - vcf_splice_df = vcf_splice_df[['Chromosome', 'Start', 'ref', 'alt', 'gene_id', 'feature', 'Strand_b', 'Start_b']] - - #Splice site position - vcf_splice_df['Start_b'] += max_distance - vcf_splice_df = vcf_splice_df.rename(columns={'Start' : 'Pos', 'Start_b' : 'splice_pos', 'Strand_b' : 'Strand'}) - - #Distance to splice site - vcf_splice_df['distance'] = np.abs(vcf_splice_df['Pos'] - vcf_splice_df['splice_pos']) - - #Choose unique SNPs by shortest distance to splice site - vcf_splice_df = vcf_splice_df.sort_values(by='distance', ascending=True).drop_duplicates(subset=['Chromosome', 'Pos', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - vcf_splice_df = vcf_splice_df.sort_values(['Chromosome', 'Pos', 'alt'], ascending=True).copy().reset_index(drop=True) - - vcf_df_filtered = vcf_splice_df.rename(columns={'Chromosome' : 'chrom', 'Pos' : 'pos', 'Strand' : 'strand'}) - vcf_df_filtered = vcf_df_filtered[['chrom', 'pos', 'ref', 'alt', 'gene_id', 'feature', 'strand', 'splice_pos', 'distance']] - - print("len(vcf_df_filtered) = " + str(len(vcf_df_filtered))) - - #Store intermediate SNPs (filtered) - vcf_df_filtered.to_csv("ge/GTEx_snps_" + tissue_name + "_splice_filtered.bed.gz", sep='\t', index=False) - - #Reload filtered SNP file - vcf_df_filtered = pd.read_csv("ge/GTEx_snps_" + tissue_name + "_splice_filtered.bed.gz", sep='\t', compression='gzip') - - #Create variant identifier - vcf_df_filtered['variant'] = vcf_df_filtered['chrom'] + "_" + vcf_df_filtered['pos'].astype(str) + "_" + vcf_df_filtered['ref'] + "_" + vcf_df_filtered['alt'] - - #Load merged fine-mapping dataframe - finemap_df = pd.read_csv(finemap_file, sep='\t')[['variant', 'pip']] - - #Join against fine-mapping dataframe - neg_df = vcf_df_filtered.join(finemap_df.set_index('variant'), on='variant', how='left') - neg_df.loc[neg_df['pip'].isnull(), 'pip'] = 0. - - #Only keep SNPs with PIP < cutoff - neg_df = neg_df.query("pip < " + str(pip_cutoff)).copy().reset_index(drop=True) - - #Store final table of negative SNPs - neg_df.to_csv("ge/GTEx_snps_" + tissue_name + "_splice_negatives.bed.gz", sep='\t', index=False) - - print("len(neg_df) = " + str(len(neg_df))) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/sqtl_make_positive_sets.py b/src/scripts/data/qtl_data/sqtl_make_positive_sets.py deleted file mode 100644 index 954ab7e..0000000 --- a/src/scripts/data/qtl_data/sqtl_make_positive_sets.py +++ /dev/null @@ -1,190 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser - -import os - -import util - -import numpy as np -import pandas as pd - -import pyranges as pr - -''' -sqtl_make_positive_sets.py - -Build tables with positive (causal) SNPs for sQTLs. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options] arg' - parser = OptionParser(usage) - #parser.add_option() - (options,args) = parser.parse_args() - - #Parameters - pip_cutoff = 0.01 - max_distance = 10000 - gene_pad = 50 - splice_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_protein_splice.gff' - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort.gtf' - - #Define tissues - tissue_names = [ - 'adipose_subcutaneous', - 'adipose_visceral', - 'adrenal_gland', - 'artery_aorta', - 'artery_coronary', - 'artery_tibial', - 'blood', - 'brain_amygdala', - 'brain_anterior_cingulate_cortex', - 'brain_caudate', - 'brain_cerebellar_hemisphere', - 'brain_cerebellum', - 'brain_cortex', - 'brain_frontal_cortex', - 'brain_hippocampus', - 'brain_hypothalamus', - 'brain_nucleus_accumbens', - 'brain_putamen', - 'brain_spinal_cord', - 'brain_substantia_nigra', - 'breast', - 'colon_sigmoid', - 'colon_transverse', - 'esophagus_gej', - 'esophagus_mucosa', - 'esophagus_muscularis', - 'fibroblast', - 'heart_atrial_appendage', - 'heart_left_ventricle', - 'kidney_cortex', - 'LCL', - 'liver', - 'lung', - 'minor_salivary_gland', - 'muscle', - 'nerve_tibial', - 'ovary', - 'pancreas', - 'pituitary', - 'prostate', - 'skin_not_sun_exposed', - 'skin_sun_exposed', - 'small_intestine', - 'spleen', - 'stomach', - 'testis', - 'thyroid', - 'uterus', - 'vagina', - ] - - #Compile positive SNP set for each tissue - for tissue_name in tissue_names : - - print("-- " + str(tissue_name) + " --") - - #Load fine-mapping table - vcf_df = pd.read_csv("txrev/GTEx_txrev_" + tissue_name + ".purity_filtered.txt.gz", sep='\t', usecols=['chromosome', 'position', 'ref', 'alt', 'variant', 'pip', 'molecular_trait_id'], low_memory=False) - - #Only keep SNPs (no indels) - vcf_df = vcf_df.loc[(vcf_df['ref'].str.len() == vcf_df['alt'].str.len()) & (vcf_df['ref'].str.len() == 1)].copy().reset_index(drop=True) - - #Only keep SNPs associated with splice events - vcf_df = vcf_df.loc[vcf_df['molecular_trait_id'].str.contains(".contained.")].copy().reset_index(drop=True) - - vcf_df['chromosome'] = 'chr' + vcf_df['chromosome'].astype(str) - vcf_df['start'] = vcf_df['position'].astype(int) - vcf_df['end'] = vcf_df['start'] + 1 - vcf_df['strand'] = "." - - vcf_df = vcf_df[['chromosome', 'start', 'end', 'ref', 'alt', 'strand', 'variant', 'pip', 'molecular_trait_id']] - vcf_df = vcf_df.rename(columns={'chromosome' : 'Chromosome', 'start' : 'Start', 'end' : 'End', 'strand' : 'Strand'}) - - print("len(vcf_df) = " + str(len(vcf_df))) - - #Load splice site annotation - splice_df = pd.read_csv(splice_file, sep='\t', names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str'], usecols=['Chromosome', 'Start', 'End', 'feature', 'feat1', 'Strand'])[['Chromosome', 'Start', 'End', 'feature', 'feat1', 'Strand']] - - #Load gene span annotation - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['Chromosome', 'havana_str', 'feature', 'Start', 'End', 'feat1', 'Strand', 'feat2', 'id_str']) - gtf_df = gtf_df.query("feature == 'gene'").copy().reset_index(drop=True) - - gtf_df['gene_id'] = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]) - - gtf_df = gtf_df[['Chromosome', 'Start', 'End', 'gene_id', 'feat1', 'Strand']].drop_duplicates(subset=['gene_id'], keep='first').copy().reset_index(drop=True) - - gtf_df['Start'] = gtf_df['Start'].astype(int) - gene_pad - gtf_df['End'] = gtf_df['End'].astype(int) + gene_pad - - #Join dataframes against gtf annotation - splice_pr = pr.PyRanges(splice_df) - gtf_pr = pr.PyRanges(gtf_df) - vcf_pr = pr.PyRanges(vcf_df) - - splice_gtf_pr = splice_pr.join(gtf_pr, strandedness='same') - vcf_gtf_pr = vcf_pr.join(gtf_pr, strandedness=False) - - splice_gtf_df = splice_gtf_pr.df[['Chromosome', 'Start', 'End', 'feature', 'gene_id', 'Strand']].copy().reset_index(drop=True) - vcf_gtf_df = vcf_gtf_pr.df[['Chromosome', 'Start', 'End', 'ref', 'alt', 'Strand', 'gene_id', 'variant', 'pip', 'molecular_trait_id']].copy().reset_index(drop=True) - - splice_gtf_df['Start'] -= max_distance - splice_gtf_df['End'] += max_distance - - #Join vcf against splice annotation - splice_gtf_pr = pr.PyRanges(splice_gtf_df) - vcf_gtf_pr = pr.PyRanges(vcf_gtf_df) - - vcf_splice_pr = vcf_gtf_pr.join(splice_gtf_pr, strandedness=False) - - #Force gene_id of SNP to be same as the gene_id of the splice site - vcf_splice_df = vcf_splice_pr.df.query("gene_id == gene_id_b").copy().reset_index(drop=True) - vcf_splice_df = vcf_splice_df[['Chromosome', 'Start', 'ref', 'alt', 'gene_id', 'feature', 'Strand_b', 'Start_b', 'variant', 'pip', 'molecular_trait_id']] - - #Force gene_id of SNP to be same as the gene_id of the finemapped molecular trait - vcf_splice_df['molecular_trait_gene_id'] = vcf_splice_df['molecular_trait_id'].apply(lambda x: x.split(".")[0]) - vcf_splice_df = vcf_splice_df.query("gene_id == molecular_trait_gene_id").copy().reset_index(drop=True) - - #Splice site position - vcf_splice_df['Start_b'] += max_distance - vcf_splice_df = vcf_splice_df.rename(columns={'Start' : 'Pos', 'Start_b' : 'splice_pos', 'Strand_b' : 'Strand'}) - - #Distance to splice site - vcf_splice_df['distance'] = np.abs(vcf_splice_df['Pos'] - vcf_splice_df['splice_pos']) - - #Choose unique SNPs by shortest distance to splice site (and inverse PIP for tie-breaking) - vcf_splice_df['pip_inv'] = 1. - vcf_splice_df['pip'] - - vcf_splice_df = vcf_splice_df.sort_values(by=['distance', 'pip_inv'], ascending=True).drop_duplicates(subset=['Chromosome', 'Pos', 'ref', 'alt'], keep='first').copy().reset_index(drop=True) - vcf_splice_df = vcf_splice_df.sort_values(['Chromosome', 'Pos', 'alt'], ascending=True).copy().reset_index(drop=True) - - vcf_df_filtered = vcf_splice_df.rename(columns={'Chromosome' : 'chrom', 'Pos' : 'pos', 'Strand' : 'strand'}) - vcf_df_filtered = vcf_df_filtered[['chrom', 'pos', 'ref', 'alt', 'gene_id', 'feature', 'strand', 'splice_pos', 'distance', 'variant', 'pip', 'molecular_trait_id']] - - print("len(vcf_df_filtered) = " + str(len(vcf_df_filtered))) - - #Store intermediate SNPs (filtered) - vcf_df_filtered.to_csv("txrev/GTEx_snps_" + tissue_name + "_splice_finemapped_filtered.bed.gz", sep='\t', index=False) - - #Reload filtered SNP file - vcf_df_filtered = pd.read_csv("txrev/GTEx_snps_" + tissue_name + "_splice_finemapped_filtered.bed.gz", sep='\t', compression='gzip') - - #Only keep SNPs with PIP > cutoff - pos_df = vcf_df_filtered.query("pip > " + str(pip_cutoff)).copy().reset_index(drop=True) - - #Store final table of positive SNPs - pos_df.to_csv("txrev/GTEx_snps_" + tissue_name + "_splice_positives.bed.gz", sep='\t', index=False) - - print("len(pos_df) = " + str(len(pos_df))) - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/qtl_data/sqtl_vcfs.py b/src/scripts/data/qtl_data/sqtl_vcfs.py deleted file mode 100644 index d275a76..0000000 --- a/src/scripts/data/qtl_data/sqtl_vcfs.py +++ /dev/null @@ -1,234 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser -import os -import pdb -import time - -import numpy as np -import pandas as pd -import pyranges as pr -from tqdm import tqdm - -''' -sqtl_vcfs.py - -Generate positive and negative sQTL sets from the QTL catalog txrevise. -''' - -################################################################################ -# main -################################################################################ -def main(): - usage = 'usage: %prog [options]' - parser = OptionParser(usage) - parser.add_option('--neg_pip', dest='neg_pip', - default=0.01, type='float', - help='PIP upper limit for negative examples. [Default: %default]') - parser.add_option('--pos_pip', dest='pos_pip', - default=0.9, type='float', - help='PIP lower limit for positive examples. [Default: %default]') - parser.add_option('--match_gene', dest='match_gene', - default=0, type='int', - help='Try finding negative in same gene as positive. [Default: %default]') - parser.add_option('--match_allele', dest='match_allele', - default=0, type='int', - help='Try finding negative with same ref and alt alleles. [Default: %default]') - parser.add_option('-o', dest='out_prefix', - default='qtlcat_sqtl') - (options,args) = parser.parse_args() - - tissue_name = options.out_prefix.split('txrev_')[1] - - gtf_file = '/home/drk/common/data/genomes/hg38/genes/gencode41/gencode41_basic_nort_protein.gtf' - - # read variant table - qtlcat_df_neg = pd.read_csv("ge/GTEx_snps_" + tissue_name + "_splice_negatives.bed.gz", sep='\t') - qtlcat_df_pos = pd.read_csv("txrev/GTEx_snps_" + tissue_name + "_splice_positives.bed.gz", sep='\t') - - # read TPM bin table and construct lookup dictionaries - tpm_df = pd.read_csv('ge/GTEx_ge_' + tissue_name + "_tpms.csv", sep='\t')[['gene_id', 'tpm', 'bin_index', 'bin_index_l', 'bin_index_r']] - gene_to_tpm_dict = tpm_df.set_index('gene_id').to_dict(orient='index') - - # filter on SNPs with genes in TPM bin dict - qtlcat_df_neg = qtlcat_df_neg.loc[qtlcat_df_neg['gene_id'].isin(tpm_df['gene_id'].values.tolist())].copy().reset_index(drop=True) - qtlcat_df_pos = qtlcat_df_pos.loc[qtlcat_df_pos['gene_id'].isin(tpm_df['gene_id'].values.tolist())].copy().reset_index(drop=True) - - #Load gene span annotation (protein-coding/categorized only) - gtf_df = pd.read_csv(gtf_file, sep='\t', skiprows=5, names=['id_str']) - gtf_genes = gtf_df['id_str'].apply(lambda x: x.split("gene_id \"")[1].split("\";")[0].split(".")[0]).unique().tolist() - - # filter on SNPs with genes in GTF file - qtlcat_df_neg = qtlcat_df_neg.loc[qtlcat_df_neg['gene_id'].isin(gtf_genes)].copy().reset_index(drop=True) - qtlcat_df_pos = qtlcat_df_pos.loc[qtlcat_df_pos['gene_id'].isin(gtf_genes)].copy().reset_index(drop=True) - - bin_to_genes_dict = {} - for _, row in tpm_df.iterrows() : - - if row['bin_index'] not in bin_to_genes_dict : - bin_to_genes_dict[row['bin_index']] = [] - - bin_to_genes_dict[row['bin_index']].append(row['gene_id']) - - for sample_bin in bin_to_genes_dict : - bin_to_genes_dict[sample_bin] = set(bin_to_genes_dict[sample_bin]) - - # split molecular trait id and filter for polyadenylation (for positives) - qtlcat_df_pos['gene'] = [mti.split('.')[0] for mti in qtlcat_df_pos.molecular_trait_id] - qtlcat_df_pos['event'] = [mti.split('.')[2] for mti in qtlcat_df_pos.molecular_trait_id] - - qtlcat_df_pos = qtlcat_df_pos[qtlcat_df_pos.event == 'contained'] - qtlcat_df_pos = qtlcat_df_pos.rename(columns={'distance' : 'splice_dist'}) - - qtlcat_df_neg['molecular_trait_id'] = qtlcat_df_neg['gene_id'] + "." + "grp_0.contained.negative" - qtlcat_df_neg['gene'] = qtlcat_df_neg['gene_id'] - qtlcat_df_neg['event'] = 'contained' - qtlcat_df_neg = qtlcat_df_neg.rename(columns={'distance' : 'splice_dist'}) - - sqtl_df = pd.concat([qtlcat_df_neg, qtlcat_df_pos]).copy().reset_index(drop=True) - - # determine positive variants - sqtl_pos_df = sqtl_df[sqtl_df.pip >= options.pos_pip] - sqtl_neg_df = sqtl_df[sqtl_df.pip < options.neg_pip] - pos_variants = set(sqtl_pos_df.variant) - - neg_gene_and_allele_variants = 0 - neg_gene_variants = 0 - - neg_expr_and_allele_variants = 0 - neg_expr_variants = 0 - - unmatched_variants = 0 - - # choose negative variants - neg_variants = set() - neg_dict = {} - for pvariant in tqdm(pos_variants): - sqtl_this_df = sqtl_pos_df[sqtl_pos_df.variant == pvariant] - - neg_found = False - - # optionally prefer negative from positive's gene set - if options.match_gene == 1 and options.match_allele == 1 : - pgenes = set(sqtl_this_df.gene) - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, True) - - if neg_found : - neg_gene_and_allele_variants += 1 - - if not neg_found and options.match_gene == 1 : - pgenes = set(sqtl_this_df.gene) - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, False) - - if neg_found : - neg_gene_variants += 1 - - if not neg_found and options.match_allele == 1 : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, True) - - if not neg_found and gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_l'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_l']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, True) - - if not neg_found and gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_r'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_r']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, True) - - if neg_found : - neg_expr_and_allele_variants += 1 - - if not neg_found : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, False) - - if not neg_found and gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_l'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_l']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, False) - - if not neg_found and gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index'] != gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_r'] : - pgenes = bin_to_genes_dict[gene_to_tpm_dict[sqtl_this_df.iloc[0].gene]['bin_index_r']] - neg_found = find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, False) - - if neg_found : - neg_expr_variants += 1 - - if not neg_found : - print("[Warning] Could not find a matching negative for '" + pvariant + "'") - unmatched_variants += 1 - - print('%d positive variants' % len(pos_variants)) - print('%d negative variants' % len(neg_variants)) - print(' - %d gene-matched negatives with same alleles' % neg_gene_and_allele_variants) - print(' - %d gene-matched negatives ' % neg_gene_variants) - print(' - %d expr-matched negatives with same alleles' % neg_expr_and_allele_variants) - print(' - %d expr-matched negatives ' % neg_expr_variants) - print(' - %d unmatched negatives ' % unmatched_variants) - - pos_dict = {pv: pv for pv in pos_variants} - - # write VCFs - write_vcf('%s_pos.vcf' % options.out_prefix, sqtl_df, pos_variants, pos_dict) - write_vcf('%s_neg.vcf' % options.out_prefix, sqtl_df, neg_variants, neg_dict) - -def find_negative(neg_variants, neg_dict, pos_variants, sqtl_this_df, sqtl_neg_df, pgenes, match_allele) : - - gene_mask = np.array([gene in pgenes for gene in sqtl_neg_df.gene]) - sqtl_neg_gene_df = sqtl_neg_df[gene_mask] - - # match PAS distance - this_dist = sqtl_this_df.iloc[0].splice_dist - dist_cmp = np.abs(sqtl_neg_gene_df.splice_dist - this_dist) - dist_cmp_unique = np.sort(np.unique(dist_cmp.values)) - - this_ref = sqtl_this_df.iloc[0].ref - this_alt = sqtl_this_df.iloc[0].alt - - for ni_unique in dist_cmp_unique: - - sqtl_neg_gene_dist_df = sqtl_neg_gene_df.loc[dist_cmp == ni_unique] - - shuffle_index = np.arange(len(sqtl_neg_gene_dist_df), dtype='int32') - np.random.shuffle(shuffle_index) - - for nsqtl_i in range(len(sqtl_neg_gene_dist_df)) : - nsqtl = sqtl_neg_gene_dist_df.iloc[shuffle_index[nsqtl_i]] - - if not match_allele or (nsqtl.ref == this_ref and nsqtl.alt == this_alt): - if nsqtl.variant not in neg_variants and nsqtl.variant not in pos_variants: - - neg_variants.add(nsqtl.variant) - neg_dict[nsqtl.variant] = sqtl_this_df.iloc[0].variant - - return True - - return False - -def write_vcf(vcf_file, df, variants_write, variants_dict): - vcf_open = open(vcf_file, 'w') - print('##fileformat=VCFv4.2', file=vcf_open) - print('##INFO=', - file=vcf_open) - print('##INFO=', - file=vcf_open) - print('##INFO=', - file=vcf_open) - cols = ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] - print('\t'.join(cols), file=vcf_open) - - variants_written = set() - - for v in df.itertuples(): - if v.variant in variants_write and v.variant not in variants_written: - cols = [v.chrom, str(v.pos), v.variant, v.ref, v.alt, '.', '.'] - cols += ['MT=%s;SD=%d;PI=%s' % (v.molecular_trait_id, v.splice_dist, variants_dict[v.variant])] - print('\t'.join(cols), file=vcf_open) - variants_written.add(v.variant) - - vcf_open.close() - - -################################################################################ -# __main__ -################################################################################ -if __name__ == '__main__': - main() diff --git a/src/scripts/data/training_data/Makefile b/src/scripts/data/training_data/Makefile deleted file mode 100644 index 170222b..0000000 --- a/src/scripts/data/training_data/Makefile +++ /dev/null @@ -1,47 +0,0 @@ -FASTA_HUMAN=$$HG38/assembly/ucsc/hg38.ml.fa -GAPS_HUMAN=$$HG38/assembly/ucsc/hg38_gaps.bed -UMAP_HUMAN=$$HG38//mappability/umap_k36_t10_l32.bed -BLACK_HUMAN=$$HG38/blacklist/blacklist_hg38_all.bed - -FASTA_MOUSE=$$MM10/assembly/ucsc/mm10.ml.fa -GAPS_MOUSE=$$MM10/assembly/ucsc/mm10_gaps.bed -UMAP_MOUSE=$$MM10//mappability/umap_k36_t10_l32.bed -BLACK_MOUSE=$$MM10/blacklist/blacklist_mm10_all.bed - -ALIGN=$$HG38/align/hg38.mm10.syn.net.gz - -OUT=/scratch3/drk/seqnn/data/v9 - -# LENGTH=393216 -# TSTRIDE=43691 # (393216-2*131072)/3 -# CROP=131072 - -LENGTH=524288 -TSTRIDE=49173 # (524288-2*163840)/4 + 21 -CROP=163840 -WIDTH=32 -FOLDS=8 - -AOPTS=--break 2097152 -c $(CROP) --nf 524288 --no 393216 -l $(LENGTH) --stride $(TSTRIDE) -f $(FOLDS) --umap_t 0.5 -w $(WIDTH) -DOPTS=-c $(CROP) -d 2 -f $(FOLDS) -l $(LENGTH) -p 64 -r 16 --umap_clip 0.5 -w $(WIDTH) - - -all: $(OUT)/hg38/tfrecords/train-0.tfr $(OUT)/mm10/tfrecords/train-0.tfr - -umap_human.bed: - cat $(UMAP_HUMAN) $(BLACK_HUMAN) | awk 'BEGIN {OFS="\t"} {print $$1, $$2, $$3}' | bedtools sort -i - | bedtools merge -i - > umap_human.bed - -umap_mouse.bed: - cat $(UMAP_MOUSE) $(BLACK_MOUSE) | awk 'BEGIN {OFS="\t"} {print $$1, $$2, $$3}' | bedtools sort -i - | bedtools merge -i - > umap_mouse.bed - -targets_human.txt targets_mouse.txt: - ./make_targets.py - -$(OUT)/hg38/sequences.bed $(OUT)/mm10/sequences.bed: umap_human.bed umap_mouse.bed - basenji_data_align.py -a hg38,mm10 -g $(GAPS_HUMAN),$(GAPS_MOUSE) -u umap_human.bed,umap_mouse.bed $(AOPTS) -o $(OUT) $(ALIGN) $(FASTA_HUMAN),$(FASTA_MOUSE) - -$(OUT)/hg38/tfrecords/train-0.tfr: $(OUT)/hg38/sequences.bed targets_human.txt - basenji_data.py --restart $(DOPTS) -b $(BLACK_HUMAN) -o $(OUT)/hg38 $(FASTA_HUMAN) -u umap_human.bed targets_human.txt - -$(OUT)/mm10/tfrecords/train-0.tfr: $(OUT)/mm10/sequences.bed targets_mouse.txt - basenji_data.py --restart $(DOPTS) -b $(BLACK_MOUSE) -o $(OUT)/mm10 $(FASTA_MOUSE) -u umap_mouse.bed targets_mouse.txt diff --git a/src/scripts/data/training_data/README.md b/src/scripts/data/training_data/README.md deleted file mode 100644 index 7c2751e..0000000 --- a/src/scripts/data/training_data/README.md +++ /dev/null @@ -1,11 +0,0 @@ -## Data processing & Training - -Processing of ENCODE, GTEx, FANTOM5, and CATlas training data is done through a Makefile. It requires a number of auxiliary files (e.g. genome alignments), which can be downloaded from the Borzoi training data bucket [here](https://storage.googleapis.com/borzoi-paper/data/) (GCP).
- -The Makefile relies on the script 'basenji_data.py' from the [basenji repository](https://github.com/calico/basenji/blob/master/bin/basenji_data.py), which in turn calls the scripts 'basenji_data_read.py' and 'basenji_data_write.py' from the same repo, in order to (1) read coverage data (from bigwig-like files) along with a matched segment from a fasta genome file, and (2) write the (one-hot coded) sequence along with coverage values into compressed TF records.
- -*Notes*: -- The attached Makefile shows the exact commands used to call basenji_data.py and other related scripts to create the specific training data for the published model. -- The script(s) take as input a fasta genome file, optional blacklist+unmappable region files, as well as a .txt file where each row points to a bigwig coverage file location (see for [this file](https://raw.githubusercontent.com/calico/borzoi/main/examples/targets_human.txt)).
- -The model training is done through the script 'hound_train.py' from the [baskerville repository](https://github.com/calico/baskerville/blob/main/src/baskerville/scripts/hound_train.py). Most of the training parameters are set through a .json file that is supplied to the script. The published model's parameter file can be found [here](https://storage.googleapis.com/seqnn-share/borzoi/params.json).
diff --git a/src/scripts/idx_genome.py b/src/scripts/idx_genome.py new file mode 100755 index 0000000..92127b0 --- /dev/null +++ b/src/scripts/idx_genome.py @@ -0,0 +1,32 @@ +#!/usr/bin/env python +from optparse import OptionParser +import os +import sys +import pyfaidx + +''' +idx_genome.py + +Create .fai index file for input .fa. +''' + +################################################################################ +# main +################################################################################ +def main(): + usage = 'usage: %prog [options] ' + parser = OptionParser(usage) + (options, args) = parser.parse_args() + + if len(args) != 1: + parser.error('Must provide input fasta file') + else: + genome_fa = args[0] + + pyfaidx.Faidx(genome_fa) + +################################################################################ +# __main__ +################################################################################ +if __name__ == '__main__': + main() diff --git a/src/scripts/pygene.py b/src/scripts/pygene.py new file mode 100755 index 0000000..86cae4f --- /dev/null +++ b/src/scripts/pygene.py @@ -0,0 +1,324 @@ +#!/usr/bin/env python +from optparse import OptionParser + +import gzip +import pdb + +''' +pygene + +Classes and methods to manage genes in GTF format. +''' + +################################################################################ +# Classes +################################################################################ +class GenomicInterval: + def __init__(self, start, end, chrom=None, strand=None): + self.start = start + self.end = end + self.chrom = chrom + self.strand = strand + + def __eq__(self, other): + return self.start == other.start + + def __lt__(self, other): + return self.start < other.start + + def __cmp__(self, x): + if self.start < x.start: + return -1 + elif self.start > x.start: + return 1 + else: + return 0 + + def __str__(self): + if self.chrom is None: + label = '[%d-%d]' % (self.start, self.end) + else: + label = '%s:%d-%d' % (self.chrom, self.start, self.end) + return label + + +class Transcript: + def __init__(self, chrom, strand, kv): + self.chrom = chrom + self.strand = strand + self.kv = kv + self.exons = [] + self.cds = [] + self.utrs3 = [] + self.utrs5 = [] + self.sorted = False + self.utrs_defined = False + + def add_cds(self, start, end): + self.cds.append(GenomicInterval(start,end)) + + def add_exon(self, start, end): + self.exons.append(GenomicInterval(start,end)) + + def define_utrs(self): + self.utrs_defined = True + + if len(self.cds) == 0: + self.utrs3 = self.exons + + else: + assert(self.sorted) + + # reset UTR lists + self.utrs5 = [] + self.utrs3 = [] + + # match up exons and CDS + ci = 0 + for ei in range(len(self.exons)): + # left initial + if self.exons[ei].end < self.cds[ci].start: + utr = GenomicInterval(self.exons[ei].start, self.exons[ei].end) + if self.strand == '+': + self.utrs5.append(utr) + else: + self.utrs3.append(utr) + + # right initial + elif self.cds[ci].end < self.exons[ei].start: + utr = GenomicInterval(self.exons[ei].start, self.exons[ei].end) + if self.strand == '+': + self.utrs3.append(utr) + else: + self.utrs5.append(utr) + + # overlap + else: + # left overlap + if self.exons[ei].start < self.cds[ci].start: + utr = GenomicInterval(self.exons[ei].start, self.cds[ci].start-1) + if self.strand == '+': + self.utrs5.append(utr) + else: + self.utrs3.append(utr) + + # right overlap + if self.cds[ci].end < self.exons[ei].end: + utr = GenomicInterval(self.cds[ci].end+1, self.exons[ei].end) + if self.strand == '+': + self.utrs3.append(utr) + else: + self.utrs5.append(utr) + + # increment up to last + ci = min(ci+1, len(self.cds)-1) + + def fasta_cds(self, fasta_open, stranded=False): + assert(self.sorted) + gene_seq = '' + for exon in self.cds: + exon_seq = fasta_open.fetch(self.chrom, exon.start-1, exon.end) + gene_seq += exon_seq + if stranded and self.strand == '-': + gene_seq = rc(gene_seq) + return gene_seq + + def fasta_exons(self, fasta_open, stranded=False): + assert(self.sorted) + gene_seq = '' + for exon in self.exons: + exon_seq = fasta_open.fetch(self.chrom, exon.start-1, exon.end) + gene_seq += exon_seq + if stranded and self.strand == '-': + gene_seq = rc(gene_seq) + return gene_seq + + def sort_exons(self): + self.sorted = True + if len(self.exons) > 1: + self.exons.sort() + if len(self.cds) > 1: + self.cds.sort() + + def span(self): + exon_starts = [exon.start for exon in self.exons] + exon_ends = [exon.end for exon in self.exons] + return min(exon_starts), max(exon_ends) + + def tss(self): + if self.strand == '-': + return self.exons[-1].end + else: + return self.exons[0].start + + def write_gtf(self, gtf_out, write_cds=False, write_utrs=False): + for ex in self.exons: + cols = [self.chrom, 'pygene', 'exon', str(ex.start), str(ex.end)] + cols += ['.', self.strand, '.', kv_gtf(self.kv)] + print('\t'.join(cols), file=gtf_out) + if write_cds: + for cds in self.cds: + cols = [self.chrom, 'pygene', 'CDS', str(cds.start), str(cds.end)] + cols += ['.', self.strand, '.', kv_gtf(self.kv)] + print('\t'.join(cols), file=gtf_out) + if write_utrs: + assert(self.utrs_defined) + for utr in self.utrs5: + cols = [self.chrom, 'pygene', '5\'UTR', str(utr.start), str(utr.end)] + cols += ['.', self.strand, '.', kv_gtf(self.kv)] + print('\t'.join(cols), file=gtf_out) + for utr in self.utrs3: + cols = [self.chrom, 'pygene', '3\'UTR', str(utr.start), str(utr.end)] + cols += ['.', self.strand, '.', kv_gtf(self.kv)] + print('\t'.join(cols), file=gtf_out) + + def __str__(self): + return '%s %s %s %s' % (self.chrom, self.strand, kv_gtf(self.kv), ','.join([ex.__str__() for ex in self.exons])) + + +class Gene: + def __init__(self): + self.transcripts = {} + self.chrom = None + self.strand = None + self.start = None + self.end = None + + def add_transcript(self, tx_id, tx): + self.transcripts[tx_id] = tx + self.chrom = tx.chrom + self.strand = tx.strand + self.kv = tx.kv + + def span(self): + tx_spans = [tx.span() for tx in self.transcripts.values()] + tx_starts, tx_ends = zip(*tx_spans) + self.start = min(tx_starts) + self.end = max(tx_ends) + return self.start, self.end + + +class GTF: + def __init__(self, gtf_file, trim_dot=False): + self.gtf_file = gtf_file + self.genes = {} + self.transcripts = {} + self.utrs_defined = False + self.trim_dot = trim_dot + + self.read_gtf() + + def define_utrs(self): + self.utrs_defined = True + for tx in self.transcripts.values(): + tx.define_utrs() + + def read_gtf(self): + if self.gtf_file[-3:] == '.gz': + gtf_in = gzip.open(self.gtf_file, 'rt') + else: + gtf_in = open(self.gtf_file) + + # ignore header + line = gtf_in.readline() + while line[0] == '#': + line = gtf_in.readline() + + while line: + a = line.split('\t') + if a[2] in ['exon','CDS']: + chrom = a[0] + interval_type = a[2] + start = int(a[3]) + end = int(a[4]) + strand = a[6] + kv = gtf_kv(a[8]) + + # add/get transcript + tx_id = kv['transcript_id'] + if self.trim_dot: + tx_id = trim_dot(tx_id) + if not tx_id in self.transcripts: + self.transcripts[tx_id] = Transcript(chrom, strand, kv) + tx = self.transcripts[tx_id] + + # add/get gene + gene_id = kv['gene_id'] + if self.trim_dot: + gene_id = trim_dot(gene_id) + if not gene_id in self.genes: + self.genes[gene_id] = Gene() + self.genes[gene_id].add_transcript(tx_id, tx) + + # add exons + if interval_type == 'exon': + tx.add_exon(start, end) + elif interval_type == 'CDS': + tx.add_cds(start, end) + + line = gtf_in.readline() + + gtf_in.close() + + # sort transcript exons + for tx in self.transcripts.values(): + tx.sort_exons() + + def write_gtf(self, out_gtf_file, write_cds=False, write_utrs=False): + if write_utrs and not self.utrs_defined: + self.define_utrs() + + gtf_out = open(out_gtf_file, 'w') + for tx in self.transcripts.values(): + tx.write_gtf(gtf_out, write_cds, write_utrs) + gtf_out.close() + + +################################################################################ +# Methods +################################################################################ +def gtf_kv(s): + """Convert the last gtf section of key/value pairs into a dict.""" + d = {} + + a = s.split(';') + for key_val in a: + if key_val.strip(): + eq_i = key_val.find('=') + if eq_i != -1 and key_val[eq_i-1] != '"': + kvs = key_val.split('=') + else: + kvs = key_val.split() + + key = kvs[0] + if kvs[1][0] == '"' and kvs[-1][-1] == '"': + val = (' '.join(kvs[1:]))[1:-1].strip() + else: + val = (' '.join(kvs[1:])).strip() + + d[key] = val + + return d + +def kv_gtf(d): + """Convert a kv hash to str gtf representation.""" + s = '' + + if 'gene_id' in d.keys(): + s += '%s "%s"; ' % ('gene_id',d['gene_id']) + + if 'transcript_id' in d.keys(): + s += '%s "%s"; ' % ('transcript_id',d['transcript_id']) + + for key in sorted(d.keys()): + if key not in ['gene_id','transcript_id']: + s += '%s "%s"; ' % (key,d[key]) + + return s + +def trim_dot(gene_id): + """Trim the final dot suffix off a gene_id.""" + dot_i = gene_id.rfind('.') + if dot_i != -1: + gene_id = gene_id[:dot_i] + return gene_id \ No newline at end of file diff --git a/src/scripts/slurm.py b/src/scripts/slurm.py new file mode 100755 index 0000000..ab83e69 --- /dev/null +++ b/src/scripts/slurm.py @@ -0,0 +1,332 @@ +#!/usr/bin/env python +from __future__ import print_function +from optparse import OptionParser +import os, pdb, sys, subprocess, tempfile, time + +################################################################################ +# slurm.py +# +# Methods to run jobs on SLURM. +################################################################################ + + +################################################################################ +# main +################################################################################ +def main(): + usage = 'usage: %prog [options] arg' + parser = OptionParser(usage) + parser.add_option('-g', dest='go', + default=False, action='store_true', + help='Don\'t wait for the job to finish [Default: %default]') + + parser.add_option('-o', dest='out_file') + parser.add_option('-e', dest='err_file') + + parser.add_option('-J', dest='job_name') + + parser.add_option('-q', dest='queue', default='general') + parser.add_option('-n', dest='cpu', default=1, type='int') + parser.add_option('-m', dest='mem', default=None, type='int') + parser.add_option('-t', dest='time', default=None) + + (options,args) = parser.parse_args() + + cmd = args[0] + + main_job = Job(cmd, name=options.job_name, + out_file=options.out_file, err_file=options.err_file, + queue=options.queue, cpu=options.cpu, + mem=options.mem, time=options.time) + main_job.launch() + + if options.go: + time.sleep(1) + + # find the job + if not main_job.update_status: + time.sleep(1) + + # delete sbatch + main_job.clean() + + else: + time.sleep(10) + + # find the job + if not main_job.update_status(): + time.sleep(10) + + # wait for it to complete + while main_job.update_status() and main_job.status in ['PENDING','RUNNING']: + time.sleep(30) + + print('%s %s' % (main_job.name, main_job.status), file=sys.stderr) + + # delete sbatch + main_job.clean() + + +################################################################################ +# multi_run +# +# Launch and manage multiple SLURM jobs in parallel, using only one 'sacct' +# call per +################################################################################ +def multi_run(jobs, max_proc=None, verbose=False, launch_sleep=2, update_sleep=20): + total = len(jobs) + finished = 0 + running = 0 + active_jobs = [] + + if max_proc is None: + max_proc = len(jobs) + + while finished + running < total: + # launch jobs up to the max + while running < max_proc and finished+running < total: + # launch + jobs[finished+running].launch() + time.sleep(launch_sleep) + if verbose: + print(jobs[finished+running].name, jobs[finished+running].cmd, file=sys.stderr) + + # save it + active_jobs.append(jobs[finished+running]) + running += 1 + + # sleep + time.sleep(update_sleep) + + # update all statuses + multi_update_status(active_jobs) + + # update active jobs + active_jobs_new = [] + for i in range(len(active_jobs)): + if active_jobs[i].status in ['PENDING', 'RUNNING']: + active_jobs_new.append(active_jobs[i]) + else: + if verbose: + print('%s %s' % (active_jobs[i].name, active_jobs[i].status), file=sys.stderr) + + running -= 1 + finished += 1 + + active_jobs = active_jobs_new + + + # wait for all to finish + while active_jobs: + # sleep + time.sleep(update_sleep) + + # update all statuses + multi_update_status(active_jobs) + + # update active jobs + active_jobs_new = [] + for i in range(len(active_jobs)): + if active_jobs[i].status in ['PENDING', 'RUNNING']: + active_jobs_new.append(active_jobs[i]) + else: + if verbose: + print('%s %s' % (active_jobs[i].name, active_jobs[i].status), file=sys.stderr) + + running -= 1 + finished += 1 + + active_jobs = active_jobs_new + + +################################################################################ +# multi_update_status +# +# Update the status for multiple jobs at once. +################################################################################ +def multi_update_status(jobs, max_attempts=3, sleep_attempt=5): + # reset all + for j in jobs: + j.status = None + + # try multiple times because sometimes it fails + attempt = 0 + while attempt < max_attempts and [j for j in jobs if j.status == None]: + if attempt > 0: + time.sleep(sleep_attempt) + + sacct_str = subprocess.check_output('sacct', shell=True) + sacct_str = sacct_str.decode('UTF-8') + + # split into job lines + sacct_lines = sacct_str.split('\n') + for line in sacct_lines[2:]: + a = line.split() + + try: + line_id = int(a[0]) + except: + line_id = None + + # check call jobs for a match + for j in jobs: + if line_id == j.id: + # j.status = a[5] # original + j.status = a[4] # cb2 + + attempt += 1 + + +class Job: + ''' class to manage SLURM jobs. + + Notes: + -Since we have two types of machines in the GPU queue, I'm asking + for the machine type as "queue", and the "launch" method will handle it. + ''' + + def __init__(self, cmd, name, out_file=None, err_file=None, sb_file=None, + queue='standard', cpu=1, mem=None, time=None, gpu=0): + self.cmd = cmd + self.name = name + self.out_file = out_file + self.err_file = err_file + self.sb_file = sb_file + self.queue = self.translate_gpu(queue) + self.cpu = cpu + self.mem = mem + self.time = time + self.gpu = gpu + + self.id = None + self.status = None + + + def flash(self): + ''' Determine if the job can run on the flash queue by parsing the time. ''' + + day_split = self.time.split('-') + if len(day_split) == 2: + days, hms = day_split + else: + days = 0 + hms = day_split[0] + + hms_split = hms.split(':') + if len(hms_split) == 3: + hours, mins, secs = hms_split + elif len(hms_split) == 2: + hours = 0 + mins, secs = hms_split + else: + print('Cannot parse time: ', self.time, file=sys.stderr) + exit(1) + + hours_sum = 24*int(days) + int(hours) + float(mins)/60 + + return hours_sum <= 4 + + + def launch(self): + ''' Make an sbatch file, launch it, and save the job id. ''' + + # make sbatch script + if self.sb_file is None: + sbatch_tempf = tempfile.NamedTemporaryFile() + sbatch_file = sbatch_tempf.name + else: + sbatch_file = self.sb_file + sbatch_out = open(sbatch_file, 'w') + + print('#!/bin/bash\n', file=sbatch_out) + if self.gpu > 0: + if self.queue == "" or self.queue == 'gpu': + gpu_str = 'gpu' + gres_str = '--gres=gpu' + elif self.queue == 'nvidia_geforce_rtx_4090': + gpu_str = 'minigpu' + gres_str = '--gres=gpu:%s' % self.queue + else: + gpu_str = 'gpu' + gres_str = '--gres=gpu:%s' % self.queue + print('#SBATCH -p %s' % gpu_str, file=sbatch_out) + print('#SBATCH %s:%d\n' % (gres_str, self.gpu), file=sbatch_out) + else: + print('#SBATCH -p %s' % self.queue, file=sbatch_out) + print('#SBATCH -n 1', file=sbatch_out) + print('#SBATCH -c %d' % self.cpu, file=sbatch_out) + if self.name: + print('#SBATCH -J %s' % self.name, file=sbatch_out) + if self.out_file: + print('#SBATCH -o %s' % self.out_file, file=sbatch_out) + if self.err_file: + print('#SBATCH -e %s' % self.err_file, file=sbatch_out) + if self.mem: + print('#SBATCH --mem %d' % self.mem, file=sbatch_out) + if self.time: + print('#SBATCH --time %s' % self.time, file=sbatch_out) + print(self.cmd, file=sbatch_out) + + sbatch_out.close() + + # launch it; check_output to get the id + launch_str = subprocess.check_output('sbatch %s' % sbatch_file, shell=True) + + # e.g. "Submitted batch job 13861989" + self.id = int(launch_str.split()[3]) + + + def translate_gpu(self, queue_gpu): + """Translate concise GPU labels to their full versions, + or propagate the given label.""" + translation = { + 'p100': 'tesla_p100-pcie-16gb', + 'tesla': 'tesla_p100-pcie-16gb', + 'geforce': 'nvidia_geforce_gtx_1080_ti', + 'gtx1080': 'nvidia_geforce_gtx_1080_ti', + 'titan': 'titan_rtx', + 'quadro': 'quadro_rtx_8000', + 'rtx4090': 'nvidia_geforce_rtx_4090' + } + return translation.get(queue_gpu, queue_gpu) + + + def update_status(self, max_attempts=3, sleep_attempt=5): + ''' Use 'sacct' to update the job's status. Return True if found and False if not. ''' + + status = None + + attempt = 0 + while attempt < max_attempts and status == None: + if attempt > 0: + time.sleep(sleep_attempt) + + sacct_str = subprocess.check_output('sacct', shell=True) + sacct_str = sacct_str.decode('UTF-8') + + sacct_lines = sacct_str.split('\n') + for line in sacct_lines[2:]: + a = line.split() + + try: + line_id = int(a[0]) + except: + line_id = None + + if line_id == self.id: + status = a[5] + + attempt += 1 + + if status == None: + return False + else: + self.status = status + return True + + +################################################################################ +# __main__ +################################################################################ +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/src/scripts/util.py b/src/scripts/util.py new file mode 100755 index 0000000..58b46a3 --- /dev/null +++ b/src/scripts/util.py @@ -0,0 +1,120 @@ +#!/usr/bin/env python +from __future__ import print_function +#import pdb +import operator, os, sys, subprocess, time + +############################################################ +# util +# +# Helpful methods that are difficult to categorize. +############################################################ + +############################################################ +# condorify +############################################################ +def condorify(cmds): + return ['runCmd -c "%s"' % c for c in cmds] + +############################################################ +# slurmify +############################################################ +def slurmify(cmds, mem_mb=None): + if mem != None: + mem_str = '--mem %d' % mem_mb + else: + mem_str = '' + + return ['srun -p general -n 1 %s "%s"' % (mem_str,c) for c in cmds] + +############################################################ +# exec_par +# +# Execute the commands in the list 'cmds' in parallel, but +# only running 'max_proc' at a time. +############################################################ +def exec_par(cmds, max_proc=None, verbose=False): + total = len(cmds) + finished = 0 + running = 0 + p = [] + + if max_proc == None: + max_proc = len(cmds) + + if max_proc == 1: + while finished < total: + if verbose: + print(cmds[finished], file=sys.stderr) + op = subprocess.Popen(cmds[finished], shell=True) + os.waitpid(op.pid, 0) + finished += 1 + + else: + while finished + running < total: + # launch jobs up to max + while running < max_proc and finished+running < total: + if verbose: + print(cmds[finished+running], file=sys.stderr) + p.append(subprocess.Popen(cmds[finished+running], shell=True)) + # print('Running %d' % p[running].pid) + running += 1 + + # are any jobs finished + new_p = [] + for i in range(len(p)): + # print('POLLING', i, p[i].poll()) + if p[i].poll() != None: + running -= 1 + finished += 1 + else: + new_p.append(p[i]) + + # if none finished, sleep + if len(new_p) == len(p): + time.sleep(1) + p = new_p + + # wait for all to finish + for i in range(len(p)): + p[i].wait() + +############################################################ +# slurm_par +# +# Execute the commands in the list 'cmds' in parallel on +# SLURM, but only running 'max_proc' at a time. +# +# Doesn't work. Jobs are allocated resources, but won't run. +# Also, I'd have to screen into login nodes, which +# isn't great because I can't get back to them. +############################################################ +def slurm_par(cmds, max_proc, queue='general', cpu=1, mem=None, out_files=None, err_files=None): + # preprocess cmds + if mem != None: + mem_str = '--mem %d' % mem + else: + mem_str = '' + + if out_files != None: + out_strs = ['-o %s' % of for of in out_files] + else: + out_strs = ['']*len(cmds) + + if err_files != None: + err_strs = ['-e %s' % ef for ef in err_files] + else: + err_strs = ['']*len(cmds) + + slurm_cmds = ['srun -p %s -n %d %s %s %s "%s"' % (queue, cpu, mem_str, out_strs[i], err_strs[i], cmds[i]) for i in range(len(cmds))] + + exec_par(slurm_cmds, max_proc, print_cmd=True) + + +############################################################ +# sort_dict +# +# Sort a dict by the values, returning a list of tuples +############################################################ +def sort_dict(hash, reverse=False): + return sorted(hash.items(), key=operator.itemgetter(1), reverse=reverse) + diff --git a/src/scripts/w5_merge.py b/src/scripts/w5_merge.py new file mode 100755 index 0000000..307cfde --- /dev/null +++ b/src/scripts/w5_merge.py @@ -0,0 +1,110 @@ +#!/usr/bin/env python +from optparse import OptionParser +import os +import sys + +import h5py +import numpy as np + +''' +w5_merge.py + +Merge wig5 files using a specified summary statistic. +''' + +################################################################################ +# main +################################################################################ +def main(): + usage = 'usage: %prog [options] ...' + parser = OptionParser(usage) + parser.add_option('-s', dest='sum_stat', + default='sum', help='Summary statistic [Default: %default]') + parser.add_option('-v', dest='verbose', + default=False, action='store_true') + parser.add_option('-w', dest='overwrite', + default=False, action='store_true') + parser.add_option('-z', dest='gzip', + default=False, action='store_true') + (options,args) = parser.parse_args() + + if len(args) < 3: + parser.error('Must provide output and two or more input wig5.') + else: + out_w5_file = args[0] + in_w5_files = args[1:] + + compression_args = {} + if options.gzip: + compression_args['compression'] = 'gzip' + compression_args['shuffle'] = True + + # open input wig5 + in_w5_opens = [h5py.File(iwf) for iwf in in_w5_files] + in_num = len(in_w5_opens) + + # take keys union + in_keys = set() + for in_w5_open in in_w5_opens: + in_keys |= in_w5_open.keys() + + # open output file + if os.path.isfile(out_w5_file) and not options.overwrite: + parser.error('%s exists. Please remove.' % out_w5_file) + out_w5_open = h5py.File(out_w5_file, 'w') + + for out_key in in_keys: + if options.verbose: + print(out_key) + + # initialize array + for i in range(in_num): + if out_key in in_w5_opens[i]: + in_key_len = len(in_w5_opens[i][out_key]) + break + in_key_data = np.zeros((in_num,in_key_len), dtype='float32') + + # read data + for i in range(in_num): + if out_key in in_w5_opens[i]: + in_key_data[i] = np.array(in_w5_opens[i][out_key]) + else: + print('%s missing %s' % (in_w5_files[i], out_key), file=sys.stderr) + + # summarize + if options.sum_stat == 'sum': + out_key_data = in_key_data.sum(axis=0) + + elif options.sum_stat == 'mean': + out_key_data = in_key_data.mean(axis=0) + + elif options.sum_stat == 'geo-mean': + in_key_data_log = np.log(in_key_data) + in_key_data_log_mean = in_key_data_log.mean(axis=0) + out_key_data = np.exp(in_key_data_log_mean) + + elif options.sum_stat == 'sqrt-mean': + in_key_data_sqrt = in_key_data**0.5 + in_key_data_sqrt_mean = in_key_data_sqrt.mean(axis=0) + out_key_data = in_key_data_sqrt_mean**2 + + else: + print('Cannot identify summary statistic %s' % options.sum_stat) + + # carefully decrease resolution + out_key_data = np.clip(out_key_data, np.finfo(np.float16).min, np.finfo(np.float16).max) + out_key_data = out_key_data.astype('float16') + + # write + out_w5_open.create_dataset(out_key, data=out_key_data, + dtype='float16', **compression_args) + + out_w5_open.close() + + + +################################################################################ +# __main__ +################################################################################ +if __name__ == '__main__': + main() diff --git a/src/scripts/w5_qc.py b/src/scripts/w5_qc.py new file mode 100755 index 0000000..0d007e6 --- /dev/null +++ b/src/scripts/w5_qc.py @@ -0,0 +1,322 @@ +#!/usr/bin/env python +from optparse import OptionParser + +from collections import OrderedDict +import os +import pdb +import sys + +import h5py +from intervaltree import IntervalTree +import numpy as np +from scipy.ndimage.filters import maximum_filter1d +from sklearn.mixture import GaussianMixture + +import matplotlib +matplotlib.use('agg') +import matplotlib.pyplot as plt +import seaborn as sns + +''' +w5_qc.py + +Create a QC report for a Wig5 file. +''' + +################################################################################ +# main +################################################################################ +def main(): + usage = 'usage: %prog [options] ' + parser = OptionParser(usage) + parser.add_option('-b', dest='blacklist_bed', + default='/home/drk/common/data/genomes/hg38/blacklist/blacklist_hg38_all.bed', + help='Blacklist BED file for annotating max regions.') + parser.add_option('-c', dest='chrs', + help='Process only the given comma-separated chromosomes') + parser.add_option('-g', dest='genes_bed', + help='Genes BED file for annotating max regions.') + parser.add_option('-m', dest='max_pool', + default=512, type='int', + help='Max pool window to report max values') + parser.add_option('-n', dest='max_n', + default=100, type='int', + help='Number of maximum coverage positions [Default: %default]') + parser.add_option('-o', dest='out_dir', default='w5_qc') + parser.add_option('-p', dest='pool', + default=32, type='int', + help='Average pool window to reduce dimensionality [Default: %default]') + (options,args) = parser.parse_args() + + if len(args) != 1: + parser.error('Must provide Wig5.') + else: + w5_file = args[0] + + if not os.path.isdir(options.out_dir): + os.mkdir(options.out_dir) + + w5_open = h5py.File(w5_file, 'r') + + ############################################################ + # choose chromosomes + + if options.chrs is None: + options.chrs = list(w5_open.keys()) + options.chrs = [] + for chrm in w5_open.keys(): + if chrm in ['chrM','chrEBV']: + continue + if chrm.startswith('chrUn'): + continue + if chrm.find('random') != -1: + continue + options.chrs.append(chrm) + else: + chrs_str = options.chrs + options.chrs = [] + for chrm in chrs_str.split(','): + if chrm in w5_open: + options.chrs.append(chrm) + else: + print('Chromosome %s not found in %s' % (chrm, w5_file), file=sys.stderr) + + ############################################################ + # read genome coverage + + nan_out = open('%s/nan.txt' % options.out_dir, 'w') + + chr_lens = OrderedDict() + genome_cov = [] + + for chrm in options.chrs: + # read chromosome coverage + chr_cov = np.array(w5_open[chrm], dtype='float16') + + # truncate to fit reshape here and below + pool_max = max(options.pool, options.max_pool) + chr_mod = len(chr_cov) % pool_max + chr_cov = chr_cov[:-chr_mod] + + # handle nan + chr_nan = np.mean(np.isnan(chr_cov), dtype='float64') + print('%-5s\t%7.2e' % (chrm, chr_nan), file=nan_out) + chr_cov = np.nan_to_num(chr_cov) + + # save chromosome + chr_lens[chrm] = len(chr_cov) + + # take means across windows + chr_cov_pool = np.mean(np.reshape(chr_cov, (-1, options.pool)), axis=1) + + # append to genome coverage + genome_cov.append(chr_cov_pool) + + genome_cov = np.concatenate(genome_cov) + + nan_out.close() + + ############################################################ + # plot distributions + + zero_mask = (genome_cov == 0) + zero_pct = np.mean(zero_mask) + + zero_out = open('%s/zero.txt' % options.out_dir, 'w') + print(zero_pct, file=zero_out) + zero_out.close() + + sample_size = min((~zero_mask).sum(), 200000) + sample_cov = np.random.choice(genome_cov[~zero_mask], size=sample_size, replace=False) + + plt.figure() + sns.distplot(sample_cov) + plt.savefig('%s/dist.pdf' % options.out_dir) + plt.close() + + plt.figure() + sns.distplot(np.sqrt(sample_cov)) + plt.savefig('%s/dist_sqrt.pdf' % options.out_dir) + plt.close() + + plt.figure() + sns.distplot(np.log(sample_cov+1)) + plt.savefig('%s/dist_log.pdf' % options.out_dir) + plt.close() + + ############################################################ + # histogram values + # (which help identify sparse, poorly normalized files) + + # find largest chromosome + chr_list = list(chr_lens.keys()) + lens_list = list(chr_lens.values()) + max_len_i = np.argmax(lens_list) + max_chr = chr_list[max_len_i] + + # read coverage + max_chr_cov = np.nan_to_num(w5_open[max_chr]) + + # count values + unique_cov, counts_cov = np.unique(max_chr_cov, return_counts=True) + + # write + hist_out = open('%s/hist.txt' % options.out_dir, 'w') + for i in range(len(unique_cov)): + print('%-4d\t%7.4f\t%9d' % (i, unique_cov[i], counts_cov[i]), file=hist_out) + hist_out.close() + + + ############################################################ + # counts at thresholds + + counts_out = open('%s/tcounts.txt' % options.out_dir, 'w') + for t in [4, 8, 16, 32, 64, 128, 256, 512]: + tcount = np.sum(genome_cov > t) + tpct = np.mean(genome_cov > t) + print('%-3d\t%8d\t%.2e' % (t, tcount, tpct), file=counts_out) + counts_out.close() + + ############################################################ + # compute genome percentiles + + pcts = np.array([.001, .01, .05, .25, .50, .75, .95, .99, .999]) + cov_pcts = np.percentile(genome_cov, 100*pcts) + + pcts_out = open('%s/percentiles.txt' % options.out_dir, 'w') + for i in range(len(pcts)): + print('%5.3f\t%7.3f' % (pcts[i], cov_pcts[i]), file=pcts_out) + pcts_out.close() + + ############################################################ + # compute genome and chromosome means + + means_out = open('%s/means.txt' % options.out_dir, 'w') + + genome_cov_mean = np.mean(genome_cov, dtype='float64') + print('%-5s\t%9d\t%6f\t%5.3f' % ('whole', 1, genome_cov_mean, 1.0), file=means_out) + + for chrm in options.chrs: + chr_cov = np.nan_to_num(w5_open[chrm]) + + # compute chromosome coverage mean and ratio + chr_cov_mean = np.mean(chr_cov, dtype='float64') + chr_ratio = chr_cov_mean / genome_cov_mean + print('%-23s\t%9d\t%6f\t%5.3f' % (chrm, len(chr_cov), chr_cov_mean, chr_ratio), file=means_out) + + means_out.close() + + ############################################################ + # compute genome and chromosome means + + # blacklist annotation + blacklist_trees = bed_chr_trees(options.blacklist_bed) + + # genes annotation + gene_trees = bed_chr_trees(options.genes_bed) + + # reshape + pool_mod = options.max_pool % options.pool + if pool_mod != 0: + old_pool = options.max_pool + options.max_pool -= pool_mod + print('Modifying max pool %d to %d to be divisible with avg pool.' % (old_pool, options.max_pool), file=sys.stderr) + add_pool = options.max_pool // options.pool + genome_cov_maxp = np.max(np.reshape(genome_cov, (-1,add_pool)), axis=1) + + max_out = open('%s/max.txt' % options.out_dir, 'w') + + mi = 0 + while mi < options.max_n: + max_i = np.argmax(genome_cov_maxp) + genome_i = max_i*options.max_pool + chrm, pos = genome_chr_pos(genome_i, chr_lens) + + annotations = [] + + # annotate blacklist + blacklist_chr_tree = blacklist_trees.get(chrm, IntervalTree()) + if blacklist_chr_tree[pos:pos+options.max_pool]: + annotations.append('blacklist') + + # annotate genes + gene_chr_tree = gene_trees.get(chrm, IntervalTree()) + if gene_chr_tree[pos:pos+options.max_pool]: + annotations.append('gene') + + ann_str = ','.join(annotations) + + print('%-5s\t%9d\t%7f\t%s' % (chrm, pos, genome_cov_maxp[max_i], ann_str), file=max_out) + + # zero the coverage so we don't pick it again + genome_cov_maxp[max_i] = 0 + + # next max + mi += 1 + + max_out.close() + + w5_open.close() + + +def bed_chr_trees(bed_file): + """Return a dict mapping chromosomes to IntervalTrees.""" + chr_trees = {} + if bed_file is not None: + for line in open(bed_file): + a = line.split() + chrm = a[0] + start = int(a[1]) + end = int(a[2]) + + if chrm not in chr_trees: + chr_trees[chrm] = IntervalTree() + + chr_trees[chrm][start:end] = True + + return chr_trees + + +def genome_chr_pos(gi, chr_lens): + """ Compute chromosome and position for a genome index. + + Args + gi (int): Genomic index + chr_lens (OrderedDict): Chromosome lengths + + Returns: + chrm (str): Chromosome + pos (int): Position + """ + + chrms_list = list(chr_lens.keys()) + lengths_list = list(chr_lens.values()) + + # chromosome index + ci = 0 + + # helper counters + gii = 0 + cii = 0 + + # while gi is beyond this chromosome + while ci < len(lengths_list) and gi - gii > lengths_list[ci]: + # advance genome index + gii += lengths_list[ci] + + # advance chromosome + ci += 1 + + # we shouldn't be beyond the chromosomes + assert (ci < len(lengths_list)) + + # set position + pos = gi - gii + + return chrms_list[ci], pos + +################################################################################ +# __main__ +################################################################################ +if __name__ == '__main__': + main()