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Peaktools
About peaktools
Brief: peaktools, a python package & command-line tool for peak visualization from ChIP-seq and ATAC-seq data.
Home: https://github.com/wurucheng123/peaktools
License: MIT License
About Author
Name: Ru-Cheng Wu | Email: wrc1953@outlook.com
Installation
You can install peaktools via pip:
pip install peaktools-wrc
Usage
To use peaktools visualize peaks in a reference point:
peaktools reference-point \
hg38_refseq_gene_TSS_TES.protein_only.chr21.bed \
./bam_files/K562-ATACSeq-rep1.ENCFF534DCE_chr21_chr22.bam \
ATAC_heatmap.pdf ATAC_profile.pdf \
--output ./signal_ATACSeq.RefPoint.csv -p 4
To use peaktools visualize peaks in a scale region:
peaktools scale_region \
hg38_refseq_gene_TSS_TES.protein_only.chr21.bed \
./bam_files/293.ChIP.H3K4me3.rep1.ENCFF449FCR.bam \
signal_H3K4me3.ScaleRegion.csv \
./H3K4me3_heatmap.pdf ./H3K4me3_profile.pdf -p 4
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