How to predefine Chipseq peak calling peak length in MACS?

Question

[SP]

Dear All,

I have been searching for a way to tell MACS that I want to look for narrow or broad peaks. Unfortunately, I haven't figured out which parameters are responsible.

Thanks

Answer 1

[TriS]

I think you can use the --broad parameter when calling MACS2. you can also specify the cutoff using --broad-cutoff

That allows you to put together smaller (close) regions into one broader region.

ref: https://github.com/taoliu/MACS/