芯片seq主叫的简易管理
chipseqpeaks的Python项目详细描述
Chipseq峰值
一个macs2的包装器，它可以抽象出一些东西并使其更易于使用。 感谢邱华华的启发和贡献。
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
安装
pip3 install chipseqpeaks
或
pip3 install --user chipseqpeaks
API使用示例
fromchipseqpeaksimportChIPSeqPeakswithChIPSeqPeaks(<bytesobjectorpathtoBAMfile>)ascp:cp.cleans_up=Falsecp.remove_blacklisted_peaks(<path/to/blacklist.bed>)cp.write(<outputprefix>)
命令行用法示例
有关帮助文本，请参见：
chipseqpeaks-call -h
对于芯片序列：
chipseqpeaks-call --control input.bam chip.bam
对于ATAC序列：
chipseqpeaks-call --atac-seq atac.bam
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