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Mapping CLIP-seq Regions to 5'UTR, CDS, or 3'UTR

Dear Community,

I have a list of peaks (bed format) from my CLIP-seq project and I'm trying to map where each of these peaks are located with respect to an mRNA (5' or 3' UTR, or CDS). Is there a program I can use to map this all at once rather than manually?

Thank you!

clip-seq 5'utr 3'utr
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written by mb314 • mb314

4 answers

bedtools intersect with a gff file.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks! I did that, however I only got the ID, geneID, and gene_name (for example: ID=NM_002032;geneID=FTH1;gene_name=FTH1). In your experience have you gotten the location of the peak within the coding transcript (i.e. 5'UTR/3'UTR etc). It could be an issue with my gff file.

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written by mb314 • mb314

Annovar is a software that typically annotates variants, but you can use it to annotate your CLIP-Seqs. It's very smart when assigning ambiguous genomic regions.

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written by Giovanni Quinones Valdez • Giovanni Quinones Valdez

Annovar is a software that typically annotates variants, but you can use it to annotate your CLIP-Seqs. It's very smart when assigning ambiguous genomic regions.

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written by Giovanni Quinones Valdez • Giovanni Quinones Valdez

Following up in case someone has this question, I ended up using HOMER's annotatePeaks.pl. It was very easy to use with my BED6 files.

More information here: http://homer.ucsd.edu/homer/ngs/annotation.html

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written by mb314 • mb314

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