Question: pre-miRNA annotation and quantification
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gravatar for yuabrahamliu
2.5 years ago by
yuabrahamliu40
yuabrahamliu40 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.

rna-seq • 800 views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.5 years ago by yuabrahamliu40

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.

ADD REPLYlink written 2.5 years ago by Martombo2.6k
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