I am trying to analyze Pol2 ChIPseq data, and the standard MACS2/peakcounting pipeline doesn't seem to capture what I'm after, since there's binding all over the promoter and coding region. That is, I'm less interested in finding the highest point and tweaking the summits factor, and more interested in the overall concentration differences (and profile changes) across these gene bodies/promoters...kind of like an RNAseq where I keep duplicates but worry more about normalization.
What I'd like to do is feed
dba.count with a GRanges (transcripts) peakset, but I want to make sure I get the settings right. Would something like this work?:
DBA <- dba(sampleSheet=sample.sheet.csv) #sampleSheet is standard with bamReads, bamControl (and macs files) GR <- transcripts(tdxb) counts <- dba.count(DBA, GR)
summits be set to
FALSE? Maybe I'm missing something more fundamental.
Thank you in advance! Ben