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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Q: call-summits on specified regions? #289

Open erin-a-clark opened 5 years ago

erin-a-clark commented 5 years ago

Hi,

I'm using peaks called by MACS2 from within an existing pipeline that ultimately uses IDR to filter and produce a top-set of peaks. I'd like to use the --call-summits command to identify summits within those post-IDR top-set peaks to use for motif analysis. I can't figure out whether I can use the call-summits command along with prescribed regions (e.g. input bam file & bed file to get summits only on the bed file)?

Thank you for your help!

taoliu commented 5 years ago

@erin-a-clark Even if you don't specify --call-summits (or use the subcommand refinepeak), MACS will still report summits based on the pileup values in the output. The only difference is that --call-summits will invoke SPP-like way to 'refine' the summits and sometimes it doesn't provide better results than the default behavior. If you are interested in summits in IDR peaks, you can take the IDR peaks in BED file and overlap them with MACS2 summit output (e.g. NAME_summits.bed) using bedtools.