Software package for iCLIP data analysis

Question

[anastazie.d]

Hi, I am newbie in RNA-Seq analysis and I need to analyze iCLIP data.

Do you have any ideas about suitable R package or any other tools for statistical analysis of iCLIP data (normalization of iCLIP data particularly)?

Thanks

Answer 1

[Jason]

I would check out the tools on this website for normalization of CLIP and RIP-seq data.

And although HOMER does not offer normalization you may want to check it out for making graphs or calculating reads per gene, UTR, intron, etc. I've heard HTSeq can also be helpful too, but I'm not sure about doing normalization with it.

Good luck!