Question: Does RIP-Seq really produce peaks ?
0
gravatar for clausndh
4.1 years ago by
clausndh50
European Union
clausndh50 wrote:

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.

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by clausndh50

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

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Devon Ryan88k
0
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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...

ADD COMMENTlink written 4.1 years ago by Devon Ryan88k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 736 users visited in the last hour