Question: pre-miRNA annotation and quantification
1
yuabrahamliu • 60 wrote:
Hi all, I have a question about pre-miRNA, because I need to quantify pre-miRNA expression level.
I think the first thing I need to do is to make clear of the pre-miRNA annotation and their coordinates, but I really don't know how to get these information. Is there any GTF files on pre-miRNA, or any program can extract them?
The other question of mine is that. From the miRNA-seq data, we can quantify the RPKM of miRNA, but is it really the mature miRNA level? Don't the read counts come from both mature miRNA and pre-miRNA? So, is it need to distinguish them and is there any method to do so?
Any suggestions will be appreciated. Thank you so much.
ADD COMMENT
• link
•
modified 3.1 years ago
by
Biostar ♦♦ 20
•
written
3.1 years ago by
yuabrahamliu • 60
miRDeep2 actually tries to quantify precursor miRNAs, but it's in general a hard task, since they are characterized by a short half-life and they are usually not captured by traditional small RNA sequencing methods.