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!
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.