Question: Transcriptomic features of peaks at mature mRNA level
0
gravatar for Ezhil La
20 months ago by
Ezhil La10
United Kingdom
Ezhil La10 wrote:

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 • 647 views
ADD COMMENTlink modified 20 months ago by Carlo Yague4.5k • written 20 months ago by Ezhil La10

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.

ADD REPLYlink written 20 months ago by ATpoint18k

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.

ADD REPLYlink written 20 months ago by Ezhil La10
0
gravatar for Carlo Yague
20 months ago by
Carlo Yague4.5k
Belgium
Carlo Yague4.5k wrote:

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.

ADD COMMENTlink modified 20 months ago • written 20 months ago by Carlo Yague4.5k
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