Question: How to Find the Peak Summit Location for Broad Peaks in MACS?
0
gravatar for Neberirni
2.7 years ago by
Neberirni0
Neberirni0 wrote:

Hello,

I used broad peak calling option in MACS for histone modifications.

I am wondering why the output files do not contain the peak summit position (abs_summit). Is there a way to identify those regions?

Thanks.

summit broad peak chip-seq macs • 1.4k views
ADD COMMENTlink modified 23 months ago by ildem50 • written 2.7 years ago by Neberirni0
0
gravatar for ildem
23 months ago by
ildem50
IGH - Montpellier
ildem50 wrote:

because the peaks are "broad". MACS2 assumes histone marks do not have a summit (unlike TF binding sites which have a summit at the point TF binds to DNA).

you can try macs2 refinepeak to go back and generate summits. but they wont be too accurate for broad regions.

ADD COMMENTlink written 23 months ago by ildem50
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