Question: 3' UTRs GTF file
0
gravatar for Triple Nipple
8 weeks ago by
Triple Nipple0 wrote:

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!

expression mir utr gtf • 104 views
ADD COMMENTlink modified 8 weeks ago by Asaf6.7k • written 8 weeks ago by Triple Nipple0
2
gravatar for Asaf
8 weeks ago by
Asaf6.7k
Israel
Asaf6.7k wrote:

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.

ADD COMMENTlink written 8 weeks ago by Asaf6.7k
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