Transcriptomic features of peaks at mature mRNA level

Question

[Ezhil La]

Hi,

I have a list of peaks that I want to map into genome and get different genomic features. I would like to see whether the peaks are mapped into:

5'CAP --> 5'UTR --> CDS --> STOP CODON --> 3'UTR

Are there any programs or ways to do this?

I have already looked at ChIPpeakAnno and ChIPseeker (both in Bioconductor). Both programs map peaks into
Promoter, 5'UTR, 3'UTR, Exons, immediateDownstream and Introns.

Many thanks, Ezhil

[ATpoint]

What kind of peaks are this? You talk about genomic regions but provide transcriptomic features you want to map to. Please specify what your goal is.

[Ezhil La]

Sorry, it should be 'Transcriptomic features' not the genomic features. These are the peaks obtained after m6A modification. My goal is to see the distribution of peaks on those transciptomic features.

Answer 1

[Carlo Yague]

You can try bedtools intersect. Given a set of peaks (in bed format for instance) and an annotation file, this can give you the features covered by the peaks.