Identify miRNA from deep RNA sequencing

Question

[hana]

I have deep RNA sequences of human one cell line (100bp,paired-end). I used the reference annotation from Gencode (version 22) for transcript assembly of my sequences and identified more than 200 annotated miRNA in my datasets. I would like to know are this miRNA are reliable?

As I did not performed small RNA sequencing , how I can report theses mi RNA?

[Nicolas Rosewick]

you can't in fact if you didn't do smallRNA-Seq.

Answer 1

[Chirag Nepal]

As the sequenced library is 100bp pair-end sequences, which is larger than the size of mature miRNAs (~22nt), thus it may not be the best option, as there might be two problems. 1) Due to longer size of RNA, library may not be enriched for miRNAs. 2) Even for the ones you detect sequence reads, it will be hard to tell the exact start and end position of miRNAs.

You could actually look for pri-miRNA instead and describe their characteristic features.

Check this paper: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms /// Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

[hana]

Thank you for your reply. So may I do gene target and functional prediction for those pri-miRNA?