I typically use DESeq2 to compare a Salmon-generated counts table, wherein counts are binned into pre-annotated regions (e.g. Gene A, Gene B, etc..). Binning in this manner has its limitations. For instance, if multiple peaks exist within a given annotation and Condition A causes a loss of one peak but retains the others, a difference may not be identified.
As a next step, I would like to use an undirected peak calling method, such as MACS2, to identify peaks in my dataset. These peaks would then represent annotations into which Salmon binned reads and which DESeq2 then analyzed for differences into counts.
I'm sure what I'm describing has been done by many, and I am hoping someone here might be able to direct me to a technical guide. I am especially unsure of how to link MACS2 peaks back to annotations to give them some relevance.
Thanks for any help!