Using MACS for RIP-seq analysis

[maria123701]

Good afternoon,

I have RIP-seq data that I am trying to analyse (J2 RNA immunoprecipitation, 80 million reads/sample, reads approx 30-100 bp, paired-end, RNA is from human cells). I am aware of some peak callers specifically developed for RIP-seq, in particular RIPseeker, but all the ones I could find are no longer being updated/no longer work. I have been recommended MACS2, but there seems to be conflicting information on whether CHIP-seq peak callers are at all suitable for RIP-seq. However, I was wondering whether there is any combination of MACS2/MACS3 parameters I can adjust to make it suitable for my data. Any recommendations? Thank you in advance!

Maria