MACS2 peak calling and diffreps

[josruirod]

Hello, we've been using diffreps to assess differential binding between two conditions in a Chip-seq analysis, thank you for the work. Additionally, we have performed macs2 peak calling at each condition

The issue is macs2 peaks rarely overlap with diffreps output regions (we've been observing 10% overlap of macs2 peaks at certain windows), and thus we were wondering whether diffrep regions are relevant enriched regions at each condition.

As we have background files available for each condition, diffreps output is providing Treatment.enr and Ctrl.enr columns. Even applying a threshold here (e.g. 2 Fold Change) the coincidence with significant macs2 peaks is low. Do you have any recommendation on what threshold to apply or how to proceed at this point?
The aim is to identify regions with differential binding activity, but also assess that these regions are relevant at each condition.

Hope you have any comment on this.
Thank you for your time