From f7f3918c3618bd12ef7e0b8081485eb13841027e Mon Sep 17 00:00:00 2001 From: Julia Joung Date: Sun, 18 Dec 2022 16:47:11 -0500 Subject: [PATCH] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 19a9e62..48d2584 100644 --- a/README.md +++ b/README.md @@ -12,9 +12,9 @@ Scripts from the Joung et al Cell 2023 manuscript on a Transcription Factor Atla - count_barcodes_10X.py counts TF barcodes from fastq - tf_input_file: csv file of all possible TF barcodes with 1 barcode per line - cell_input_file: csv file of all possible cell barcodes with 1 barcode per line - - r1_fastq_file: read 1 fastq file - - r2_fastq_file: read 2 fastq file - - output_prefix: prefix of files to write barcode count results to + - r1_fastq_file: read 1 fastq file + - r2_fastq_file: read 2 fastq file + - output_prefix: prefix of files to write barcode count results to - map_cells_10X.py maps TF isoforms to cells using the counts_cells.csv file from the count_barcodes_10X.py output - ORF_lib_barcode_map.csv: csv file of TF ORF barcode mapping to TF isoforms. Each line contains a TF barcode followed by the corresponding TF isoform - counts_cells.csv: csv file of cell barcode mapping to TF ORF barcodes. Each line contains a cell barcode followed by TF barcodes and associated