Degradome seq
This document explains how to run piPipes Degradome/CAGE/RACE-seq pipeline and how to interpret the output.
This pipeline provides analysis on (1) abundance (2) 5' feature and (3) relative distance to piRNAs for genes and transposons derived, 5' mono-phosphated transcripts using single-end or paired-end Degradome-seq reads generated by Next Generation Sequencing.
# require internet access
piPipes install -g mm9# use fastq-dump from SRATools (http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software)
# to download data and convert to fastq; require internet access
fastq-dump -F --gzip -A Pillai.CAGE.miwi_het.testis.adult SRR363963
# to analyze the cleavage signature between small RNA and degradome/RACE, we also need
# download the small RNA-seq data for the same/similar sample
fastq-dump -F -Z SRR363958 | \
cutadapt -a TCGTATGCCG -O 6 -m 18 --discard-untrimmed - | \
gzip > Pillai.SRA.wild_type.testis.adult.trimmed.fq.gzpiPipes deg
# or
piPipes deg -h# -i: input fastq or gzipped fastq for the degradome-seq (single-end)
# -g: use mouse genome mm9
# -c: number of CPUs to use
# -o: output directory
piPipes deg \
-i Pillai.CAGE.miwi_het.testis.adult.fastq.gz \
-g mm9 \
-c 8 \
-o Pillai.CAGE.miwi_het.testis.adult.piPipes_out \
1> Pillai.CAGE.miwi_het.testis.adult.piPipes.stdout \
2> Pillai.CAGE.miwi_het.testis.adult.piPipes.stderrThe purpose of degradome cloning in piRNA field is to capture the cleavage product of PIWI proteins. However, due to the ubiquitousness of 5' monophosphate and the instability of cleavage product, only a small portion of the reads correspond to the cleavage product. Then it is necessary to analyze the relative 5' to 5' distance between small RNA and degradome reads.
# Run small RNA pipeline first
# -i: input small RNA sequencing data in Fastq or gzipped Fastq format
# -g: use mouse genome mm9
# -c: number of CPUs to use
# -o: output directory
piPipes small \
-i Pillai.SRA.wild_type.testis.adult.trimmed.fq.gz \
-g mm9 \
-o Pillai.SRA.wild_type.testis.adult.piPipes_output \
-c 8 \
1> Pillai.SRA.wild_type.testis.adult.piPipes.stdout \
2> Pillai.SRA.wild_type.testis.adult.piPipes.stderr
# Run degradome pipeline with small RNA data
# -i: input Fastq or gzipped Fastq for the degradome-seq (single-end)
# -g: use mouse genome mm9
# -c: number of CPUs to use
# -o: output directory
# -s: directory with small RNA pipeline output
piPipes deg \
-i Pillai.CAGE.miwi_het.testis.adult.fastq.gz \
-g mm9 \
-s Pillai.SRA.wild_type.testis.adult.piPipes_output \
-c 8 \
-o Pillai.CAGE.miwi_het.testis.adult.piPipes_out \
1> Pillai.CAGE.miwi_het.testis.adult.piPipes.stdout \
2> Pillai.CAGE.miwi_het.testis.adult.piPipes.stderrThe output directory should contain the following folders and files:
cufflinks_output/
htseq_count/
rRNA_mapping/
input_read_files/
genome_mapping/
bigWig/
summaries/
pdfs/
bedtools_count/
gene_transposon_cluster_direct_mapping/
map_small_RNA/
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.basic_stats
bowtie_index/rRNA_mapping/ contains log files of rRNA mapping using Bowtie2
Similar to RNA-seq, degradome pipeline also removes rRNA mappable reads first.
genome_mapping/ contains output for genome mapping
# STAR output
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.SJ.out.tab
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Log.progress.out
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Log.out
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Log.final.out
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.Unmapped.out.mate1
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.STAR.log
# genome alignment file in bam format, sorted by coordinates
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.bam
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.bam.bai
# genome alignment file in bed12 format
# since degradome/CAGE requires the 5' end of the reads being precisely mapped
# alignments with soft-clipping on the 5' ends are removed
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.unique.bed12
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.bed12
# "unique bead12" file contains only unique mappers
# each line is an alignment of a sequence
$ head Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.unique.bed12
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:32:14333:13809 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:8:5133:15456 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:15:18950:16133 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:33:3872:8475 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:11:2584:14460 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:15:9578:3676 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:28:10944:3671 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:6:13520:3867 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:18:14786:3150 1 + 3218970 3219075 255,0,0 1 105 0
chr10 3218970 3219075 HWUSI-EAS702:65:FC:1:29:18350:4783 1 + 3218970 3219075 255,0,0 1 105 0
# "all bed12" file contains signals from all mappers
# each line is no longer an alignment but accumulated signal from a species alignment
# field 4: accumulated signal from multi count. for example, 26 means that there are
# 26 reads from the library can be mapped here; but they could be mapped to elsewhere as well
# field 5: accumulated signal from reads that have been apportioned to the number
# of loci they can be mapped to. For example, if a read can be mapped to 2 loci, its contribution
# is 0.5. And from all the 26 reads that can be mapped here, their contribution is 0.999...
$ head Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.bed12
chr1 100010440 100010544 26 0.999999000000000415334 - 100010440 100010544 1 1 104 0
chr1 100011803 100011908 1 0.0384615000000000026303 + 100011803 100011908 2 1 105 0
chr1 100089433 100089521 3 3 - 100089433 100089521 3 1 88 0
chr1 100101123 100101228 1 0.142857000000000011752 - 100101123 100101228 4 1 105 0
chr1 100101492 100101597 1 1 - 100101492 100101597 5 1 105 0
chr1 100101531 100101636 1 0.0500000000000000027756 - 100101531 100101636 6 1 105 0
chr1 10015089 10017223 58 58 - 10015089 10017223 7 2 55,40 0,2094
chr1 100181199 100181293 1 0.333332999999999990415 + 100181199 100181293 8 1 94 0
chr1 100184297 100184402 28 1.55263279999999959102 + 100184297 100184402 9 1 105 0
chr1 100187852 100187957 1 0.0151515000000000000374 + 100187852 100187957 10 1 105 0bedtools_count/ contains nucleotide percentage surrounding different genomic features. If small RNA data is provided, the pipeline also calculates the "cis Ping-Pong" signature between small RNA and degradome.
See the pdfs/ folder for the figure output.
# the data are used to draw percentage plots in pdfs folder
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12.intersect_with_hybrid_piRNA_Cluster_EXON.species.5end_60.percentage
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12.intersect_with_prepachytene_piRNA_Cluster_EXON.species.5end_60.percentage
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.x_rRNA.mm9.sorted.noS.all.x_rpmk_MASK.bed12.intersect_with_Zamore_NR_EXON.species.5end_60.percentagebigWig/ contains bigWig files that can be used in UCSC genome browser.
summaries/ contains summary files with statistics on different genomic feature. Note that tRNA, snoRNA et al. has been removed before doing the interacting analysis. Thus the counts in the summary table are smaller than the one in the basic.stats file.
feature total_lib_all_mapper_reads total_feature_all_mapper_reads feature_all_mapper_percentage \
feature_sense_all_mapper_reads feature_antisense_all_mapper_reads feature_all_mapper_sense_fraction \
total_lib_unique_mapper_reads total_feature_unique_mapper_reads feature_unique_mapper_percentage \
feature_sense_unique_mapper_reads feature_antisense_unique_mapper_reads \
feature_unique_mapper_sense_fraction total_lib_unique_mapper_species \
total_feature_unique_mapper_species feature_unique_mapper_percentage \
feature_sense_unique_mapper_species feature_antisense_unique_mapper_species \
feature_unique_mapper_sense_fraction
piRNA_Cluster_EXON 3643781 86474 0.024 79067 7407 0.914 49220 84057 1.708 76909 7148 0.915 47436 7722 0.163 7072 650 0.916
prepachytene_piRNA_Cluster_EXON 3643781 4931 0.001 4785 146 0.970 49220 4726 0.096 4590 136 0.971 47436 509 0.011 498 11 0.978
hybrid_piRNA_Cluster_EXON 3643781 4720 0.001 4410 310 0.934 49220 4694 0.095 4385 309 0.934 47436 494 0.010 479 15 0.970
pachytene_piRNA_Cluster_EXON 3643781 76824 0.021 69872 6952 0.910 49220 74637 1.516 67934 6703 0.910 47436 6719 0.142 6095 624 0.907gene_transposon_cluster_direct_mapping/ contains direct mapping output to transcriptome (gene + piRNA cluster + transposon concensus sequence)
as well as abundance evaluation by eXpress
# mapping output
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.gene+cluster+repBase.log
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.gene+cluster+repBase.bam
# abundance estimation by eXpress
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.gene+cluster+repBase.eXpress.log
results.xprs
params.xprsbowtie_index/ contains bowtie index build from degradome reads themselves or the sequence retrieved from the genome surrounding the 5' end of degradome reads.
They are used as an index for small RNA mapping. The coordinates tell the relative distance between small RNA and degradome.
# index was build from the degradome directly; if paired-end is used, only the \1 read is used.
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.4.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.3.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.1.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.2.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.rev.1.ebwt
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.rev.2.ebwt
# 200 nucleotide surrounding the 5' end of the degradome reads were taken out, reverse-
# complemented and used to build an index for small RNA to map
# the index was build from degradome reads assigned to different genomie features
# Note that one coordinate is used once, even more than one read can be mapped to
# this coordinate.
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.RC.ext200.unique.rev.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.4.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.3.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.2.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.rev.1.bt2
Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.RC.ext200.unique.rev.2.bt2map_small_RNA/ contains the mapping result of small RNA to (1) degradome index; (2) 401 nt (200 x 2 + 1) index
# mapping of small RNA directly to the degradome index
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.bed2
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.species.5end
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.reads.5end
# mapping of small RNA to the 401 nt index
# from left to right: distance to the cleavage site, + mapping 5' end (guide strand), - mapping 5' end (cleaved strand)
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.prepachytene_piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.hybrid_piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.pachytene_piRNA_Cluster_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NM_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.Zamore_NR_EXON.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.refSeq_GENE.species
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.species.b2.log
Pillai.SRA.wild_type.testis.adult.trimmed.x_rRNA.x_hairpin.mm9v1.all.x_rpmk_MASK.bed2.piRNA_map_to.Pillai.CAGE.miwi_het.testis.adult.fastq.gz.repeatMasker.speciespdfs/ contain the pdf outputs
Please see example figures from the Github Wiki page or our manuscript.
##Flowchart and example figures from our manuscript
