Cutoff For Broad Peaks For Macs2 Peakcaller

Question

[Dataminer]

Hi!

I was wondering if anyone here on the forum has tested for the cutoff values (macs2) that can be used for different histone marks. I know option --broad can be used when calling broad peaks but what about the cut off value (we just cannot used default for all histone marks or can we ?)

Any suggestion is welcome.

Thank you

[crysis405]

The MACS2 manual says: For broad marks, you can try 0.05 as cutoff. So I thinks that's a good place to start

[KCC]

You shouldn't even use '--broad' for all histone marks. Some are not broad like H3K4me3.