(TOBIAS) Footprint analysis for ATAC-seq data

Summary

This pipeline applies TOBIAS (v0.13.3) and output bias-corrected footprint bed files and cutsites bw files.

Additionally, if -t and -c options are given, this program will perform differential footprint analysis.

As of 3/24/2023, the MACS2 and motif database are set for human, but should be good for mouse.

Input

The input file is a tsv format containing 2 columns: bam, sample name.

Output

The job ID folder contains results for each sample and each sample result is in the sample name folder.

  1. bias-corrected bigwig files

*_corrected.bw

  1. called TF footprints

all_bound.bed

  1. differential motifs (not implemented)

Usage

Copy your bam files together with their index files .bam.bai into your working directory.

# if you haven't logged into compute node, please do hpcf_interactive

module load python/2.7.13

# generate input.tsv
run_lsf.py --guess_input --general --file_pattern bam --replace_name ".bam"

# submit jobs
run_lsf.py -f input.tsv -p tobias_footprint

# OR, you want to do differential footprint analysis, note that sample1 and sample2 should match to the input.tsv 2nd column
# not implemented run_lsf.py -f input.tsv -p tobias_footprint_diff -t sample1 -c sample2

# add -g hg19 to specificy genome version.

Reference

https://github.com/loosolab/TOBIAS

code @ github.