Since some recent publications involving MACS2 as a valuable RIP-Seq (RNA not DNA) peak caller. I tried it to use on my data. But I realize that it since its a Chip-Seq peak-caller, has issues with the paired-end calculated insert/fragment sizes. I work with poly-A selected Material (mostly mRNA lacking Introns).
So I wonder if there are any parameters where I can use actual Fragment Sizes not in a genomic setting (but based on transcript annotations)?.
Otherwise, I don't see how MACS2 can be a reasonable paired-end Peak Caller for RIP-seq analysis.
Greetings and Thanks! David