Question: Is It Possible To Extract Mirna Info From Transcripts.Gtf(Cufflinks) Using Mirbase Annotation?
0
gravatar for Alby
7.1 years ago by
Alby90
Alby90 wrote:

Hello I have trnascripts.gtf as a cufflinks output. I also downloaded the miRNA annotation in gff3 for mus musculus( ftp://mirbase.org/pub/mirbase/CURRENT/genomes/mmu.gff3)

Is it possible to get the intersection of these two files, meaning extract miRNA information from the assembled transcript?

Thanks for all your input in advance

gff3 gtf cufflinks mirna • 2.5k views
ADD COMMENTlink written 7.1 years ago by Alby90
0
gravatar for JC
7.1 years ago by
JC8.2k
Mexico
JC8.2k wrote:

Assuming your data is from regular RNAseq, you can obtain some level of information. You can obtain some expression level for the pre-miRNA forms or poly-cistronic miRNAs, specially if the miRNA is intronic, but this level will be at the level of the associated gene. In my opinion, I will not trust such quantifications, for miRNA is better to quantify only small RNAs to see the expression of the active form.

ADD COMMENTlink written 7.1 years ago by JC8.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1137 users visited in the last hour