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.
Warning: Before using chipseqpeaks, please make sure that one of the environment variables TMPDIR, TEMP, or TMP is set to an appropriate path. This is the only way to ensure MACS2 writes temporary files to the correct location, and failing to do so may cause errors on some systems. (ง •̀_•́)ง
Installation
pip install chipseqpeaks
or
pip 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
1 maintainer
Metadata
1 maintainer
Release files for chipseqpeaks 1.1.5
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Total release size: 30.7 kB
Release files / chipseqpeaks-1.1.5.tar.gz
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