(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.
bias-corrected bigwig files
*_corrected.bw
called TF footprints
all_bound.bed
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