Does RIP-Seq really produce peaks ?

Question

[clausndh]

Hi Biostar Experts,

I have to deal with RIP-Seq data.

I understand RIP-Seq in a way that the RBP bound the transcript and then the whole transcript is pulled down and sequenced. So there is no RNAase that eats away RNA sequence, as by CHIP-Seq.

If I'm right, then I don't get the point of doing peak-calling for RIP-Seq :/

So does RIP-Seq really produce peaks?

Thanks for your help.

[Devon Ryan]

You don't need a DNase with ChIP-seq, though you'll get much nicer peaks if you do.

Answer 1

[Devon Ryan]

This will depend on the protein being IPed. For example, I have a number of RIPseq experiments where I would never call peaks, because there would be none. This is because we used a RiboTag mouse to allow us to pull down actively transcribed transcripts. By the nature of the experiment we wouldn't expect much peakiness. However, if you pull down something that has a single binding motif...