How to Find the Peak Summit Location for Broad Peaks in MACS?

Question

[Neberirni]

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.

Answer 1

[ildem]

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.