Easy management of ChIP-seq peak calling
Project description
chipseqpeaks
A wrapper for MACS2 that abstracts out some things and makes it easier to use. Thanks due to Joshua Chiou for inspiration and contributions.
Installation
pip3 install chipseqpeaks
or
pip3 install --user chipseqpeaks
Example API usage
from chipseqpeaks import ChIPSeqPeaks
with ChIPSeqPeaks(<bytes object or path to BAM file>) as cp:
cp.cleans_up = False
cp.remove_blacklisted_peaks(<path/to/blacklist.bed>)
cp.write(<output prefix>)
Example command line usage
For help text, see:
chipseqpeaks-call -h
For ChIP-seq:
chipseqpeaks-call --control input.bam chip.bam
For ATAC-seq:
chipseqpeaks-call --atac-seq atac.bam
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