Extract most squenced region from RNAseq

[Piggy]

Hi

I am doing a pulldown and deep seq experiment (similar to IP seq) to figure out an RNA binding site for an RNA binding enzyme. I process my RNAseq data using Tophat/Cufflink (just like normal differenctial expression) and get the genes that are enrich when the enzyme present. But now I want to know which part of the gene sequence is most sequence (they can be potential binding site for my enzyme). Anyone know any software that are able to do that? Or maybe any similar paper I can follow? Thank you!

[cmbetts]

You might have luck using tools designed for ChIP-Seq experiments. What you're trying to do with this RNA binding enzyme has a very similar objective, finding coverage peaks and binding motifs