How to do the peak calling for introns?

Question

[PK]

Hi all,

I have to analyse the clip-seq data. i have mapped all the file and i have to do the peakcalling. The issue what i have is that i have to call the peaks only for the introns. which i don't know how to do. The one approach will be split the intron from GTF file and use the bam files to calculate the coverage but how do i call the peaks for that. can anyone have such experience or is there any other better way to do?

[ATpoint]

Call all peaks and then subset to the regions you want. Everything else totally screws up the statistics of the peak caller.

[PK]

Sure I will try.