How to do the peak calling for introns?
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3 months ago
barrypraveen ▴ 30

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?

RNAseq clipseq peakcalling • 253 views
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Call all peaks and then subset to the regions you want. Everything else totally screws up the statistics of the peak caller.

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Sure I will try.

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