Hello everyone! I am a biologist trying to analyse my generated RIP-seq data (+/- treatment, pulldown with histone biding proteins). I have performed genome mapping using HiSat2 and not sure which package to use for Peak calling. I tried Piranha, but the output from it doesn't seem right. I tried to find published work but there are not many people who have performed RIP-seq. Any suggestions regarding the peak caller would be really helpful. Also what would be the appropriate step after peak calling? Just peak annotation and motif analysis? Or no peak calling is needed. In this case how could I proceed further. I would highly appreciate any help in this direction. Thank you very much in advance.
Thanks for your comment. I tried RIPSeeker, but it a bit complicated for me as a beginner to compute it,. As is it is RNA-IP I assume there are many split reads so I performed Hisat2 mapping. But, I am still unsure of MACS2 after Hisat2