Is It Possible To Extract Mirna Info From Transcripts.Gtf(Cufflinks) Using Mirbase Annotation?

Question

[Alby]

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

Answer 1

[JC]

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.