Mapping aligned reads to UTRs

Question

[jpcchoy]

Hi everyone,

I'm trying to work out which of my aligned reads in a sorted BAM file map to UTRs.
I have a text file with transcript and CDS coordinates as follows:

name chrom strand txStart txEnd cdsStart cdsEnd
ENST00000371007.6 chr1 - 67092164 67231852 67093004 67127240
ENST00000371006.5 chr1 - 67092175 67127261 67093004 67127240
ENST00000475209.6 chr1 - 67092175 67127261 67093579 67127240
Etc...

My reads have been aligned to hg38, and the features above are also from hg38.
For each feature (transcript) I think that the region txStart - cdsStart is the 5' UTR, and the region cdsEnd - txEnd is the 3' UTR, but am not sure how to do this mapping.

Does anyone know any packages that might serve this purpose?
Please let me know! Thanks so much.

Answer 1

[Pierre Lindenbaum]

convert the transcript file to a BED file using awk and then use samtools view with option -L