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

Question

[mb314]

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!

Answer 1

[Pierre Lindenbaum]

bedtools intersect with a gff file.

[mb314]

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.

Answer 2

[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.

Answer 3

[mb314]

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