Question: Transcriptomic features of peaks at mature mRNA level
0
gravatar for Ezhil La
2.6 years 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 • 844 views
ADD COMMENTlink modified 2.6 years ago by Carlo Yague5.0k • written 2.6 years 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 2.6 years ago by ATpoint35k

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 2.6 years ago by Ezhil La10
0
gravatar for Carlo Yague
2.6 years ago by
Carlo Yague5.0k
Canada
Carlo Yague5.0k 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 2.6 years ago • written 2.6 years ago by Carlo Yague5.0k
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