3' UTRs GTF file

Question

[Triple Nipple]

Hello, I have aligned RNAseq data to reference genome and now I have a .bam file.

I want to check for the expression of the 3' UTR region of the transcripts. For this I need a .gtf file that has annotates 3' UTR regions of transcripts. How is it possible to get such file from ensembl (the sequencing data was aligned to ensembl reference mouse genome)? is this the right way of doing what I want?

thanks!

Answer 1

[Asaf]

You can get the mouse gtf file from EnsEMBL: ftp://ftp.ensembl.org/pub/release-98/gtf/mus_musculus/ The third column of the gtf file will have the name of the feature, you can filter for features that are three_prime_utr, generate a new gtf containing only 3' UTR and count the reads mapped to these features using FeaturesCount etc.