Im working with samples from ChIP-seq, and now i'm using macs2, however when i use it,
it only does the peaks to one of the three samples that i got.
Thanks and have a good day.
Are read groups (@RG) included in your BAM inputs? This will produce a single combined MACS2 output.
Please see: https://biostar.usegalaxy.org/p/16599/#26753
Thanks! Jen, Galaxy team