Normalization of CLIP peak by transcript level

Question

[Anil Kesarwani]

HI,

I am using Piranha for CLIP-Seq data analysis. I was wondering how to normalize peaks by transcript abundance (calculated as FPKM from RNA-seq). I read in several articles that normalization with transcript level could help remove spurious peaks. I therefore performed RNA-seq as well, together with CLIP-Seq for the corresponding samples. Could some body please help me out. Any response is highly appreciated.