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.
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written
by
clausndh •
1 answer
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...
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