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

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.

chip-seq macs broad peak summit
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updated by ildem • ildem • written by Neberirni • Neberirni

1 answer

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.

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written by ildem • ildem

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