README.md

atac-seq-pipeline

ATAC-seq analysis pipeline

Dependencies

• Python
• bowtie
• samtools
• bedtools
• MACS2
• numpy
• IDR

align-reads.py

call-atac.py

Usage: python run-idr.py [options] <expt prefix> <output dir> <genome sz>

Options:
  -m   : Use parameters manually specified in script.
         This option will ignore following arguments.

run-idr.py

Usage: python call-atac.py [options] <input dir> <expt prefix> <output dir> <genome sz>

Options:
  -m   : Use parameters manually specified in script.
         This option will ignore following arguments.