Entering edit mode
6.2 years ago
yuabrahamliu
▴
60
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.
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.