Question: options for RNA polymerase II-chipseq data using macs2 callpeak
1
gravatar for chenzizhen01
2.8 years ago by
chenzizhen0110
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 • 1.4k views
ADD COMMENTlink written 2.8 years ago by chenzizhen0110

What did you do in the end?

ADD REPLYlink written 3 months ago by Biojl1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 695 users visited in the last hour