Question: options for RNA polymerase II-chipseq data using macs2 callpeak
gravatar for chenzizhen01
4.3 years ago by
chenzizhen0110 wrote:

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?

chip-seq assembly • 2.0k views
ADD COMMENTlink written 4.3 years ago by chenzizhen0110

What did you do in the end?

ADD REPLYlink written 21 months ago by Biojl1.7k
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