MACS2 call large peaks


I’m currently facing a problem with MACS2 peak calling. I’m working with short genomes and when I visually analyse the Bigwig tracks generated, I clearly see some peaks that MACS2 calls as part of a larger peak. How can I solve this problem?

I attach here a screenshot for better explain.

Screenshot 2024-04-03 alle 18.23.40

Hi @bioiz

It seems that you could tune up the peak calling parameters. Or, you could explore more tools in the MACS2 package, such as refinepeak.

Links to the software documentation are at the bottom of the tool form, and there is quite a bit of scientific discussion online, including at their google group Most command-line options are implemented in the Galaxy wrapper, and annotated with the matching flags.