options for RNA polymerase II-chipseq data using macs2 callpeak
I'm dealing with RNApolyII chipseq data using MACS2.
RNApolyII chipseq data contains two kinds of peaks:narrow peaks at TSS region and broad peaks across genebody.
So, how to set options of MACS2?
DO I have to run MACS2 twice? First, run macs2 callpeak without --broad in order to find narrow peaks at TSS. Then run macs2 with --broad to find broad peaks?
If I do that, should I run MACS2 bdgdiff separately if I want to find difference between two different samples?
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chenzizhen01 •
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