Can Macs3 be used to call peaks?

[amderogatis]

Does ArchR support peak calling with the new version of Macs (Macs3) or should Macs2 still be used? Thanks!

[anaellle]

Hello ! For me it's working with Macs3, but I had to provide the path manually as the function findMacs2() is indeed looking only for Macs2

[swetansuhota]

Hi anaellle,

I am having trouble calling macs3 to archR. Could you please post in detail how you did that...thanks in advance!

Best,
Swetansu

[anaellle]

Hi Swetansu,

If I remember correctly I downloaded macs3, probably added it to my .bash_profile file and just pass the path manually to the peak calling function. But afterwards I managed to install macs2 and ended up using macs2 only. Hope it helps.