Clarification of options --keep-dup: all vs. -f FRAG in MACS3

Question

[María José]

Hi,

I’ve been reviewing the MACS3 documentation and have a question regarding the parameters --keep-dup: all and -f FRAG. Both seem to indicate that duplicates are not removed and that all tags are retained.

Could someone clarify the key differences between these two options? Specifically, how do they affect the analysis in practical terms?

Thanks for your insights!

Answer 1

[ATpoint]

As per the manual, FRAG is specific for scATAC-seq while the other option is generic.