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Transcriptomic features of peaks at mature mRNA level

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

chip-seq genome
• 2,108 views • link
updated by Carlo Yague Carlo Yague • written by Ezhil La • Ezhil La

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.

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written by ATpoint ATpoint

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.

• 0 views • link
written by Ezhil La • Ezhil La

1 answer

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.

• 0 views • link
written by Carlo Yague Carlo Yague

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