Hi guys,
I'm trying to run ChipQC with my bam files and narrowPeak files.
But I have several different version of bam files with single dataset such as mapped bam, sorted bam, markduplicated bam
Which one should I use for chipQC?
Thank you in advance,
In the case of broad peak such as H3K4me1, as broad peakcall doesn't produce _peaks.narrowPeak format file, what file should I use?
If it is _peaks.broadPeak, then what are the appropriate parameter in peak caller instead of "narrow"?