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?