The pipeline for analysis ChIP seq and RIP seq

Question

[jolin0701-dy]

Can I use the same pipeline for ChIP seq and RIP seq?

fasts-tools to do quality control

bowtie or tophat to do mapping

macs to do peaking calling.

I thinks they can be analyzed in the same pipeline but for the downstream analysis is different..

Thanks...

Answer 1

[ivivek_ngs]

If you look at this thread you can get a clear idea of how the analysis evolved over the years and that as of now it might not be a very good ploy to use ChIPSeq peak calling for the same.

It depends what you are interested to find. I have no idea of RIP-Seq but this is what I found might be useful. So it is usually dependent on the IPed protein. Having said that take a look at this thread and this link (gives quite a number of tools for RIPseq analysis)