Find the 3' utrs, 5'utrs and their counts from bam files

Question

[ilovesuperheroes1993]

Hello,

I have bam files of 8 samples (4 normal and 4 diseased), produced by alignment with novoalign (small-rna sequencing data). I have excluded the mirna from the bam files by using the following command:

bedtools intersect -v "sample.bam" "hg19_mirna.gff3" > output.bam

In this manner I have excluded the miRNA from all the samples. Now I want to find the utr (3' and 5') sequences present in the resultant bam files, and the read counts of each of the utr sequences.

Could anyone suggest a way to do this?

[Benn]

You can try featureCounts with meta-feature "UTR" level.

[ilovesuperheroes1993]

Thank you. Actually I want to get a gtf file of the utr sequences, and then count the reads using htseq-count. But I am unable to find the gtf files of 3' and 5' utrs. Do you know where I could get it?

[Benn]

at ensembl you have gtf files for many organisms. They contain "UTR" metadata (I know for human and mouse).

[ilovesuperheroes1993]

Hi, I am currently using hg19 database (Grch37 version). I am unable to find the gtf / gff3 files of the utrs of this version. Could you please link me to them? Thanks a lot

[Benn]

I recommend you upgrade to hg38! Or search in the archives somewhere.

Answer 1

[Gautier Richard]

Using biomart at ensembl you can get the 3' and 5' UTR of hg19 (image below) at this address:

https://grch37.ensembl.org/biomart/martview/

Then I guess you can get the read coverage from these sequences using for example deepTools multiBamSummary BED-file

https://deeptools.readthedocs.io/en/develop/content/tools/multiBamSummary.html