miRNA identification from RNA seq data

Question

[sa1987]

HI

i am working on RNA seq data and not small RNA data..

i want to know how to finf the miRNA from RNA seq data.

thanks in advance plz help

[Chirag Nepal]

Which protocol did you use for library preparation ? Unless you have enriched for small RNAs (by size selection of your interest, mostly 18-30 nucleotides ), most RNA-seq data is unlikely to capture miRNAs. RNA-seq data might be 70-100 bases long, even after excluding primers/adapter, much longer than mature miRNA length, and thus such reads should not be used to quantify miRNA.

Answer 1

[Satyajeet Khare]

RNA-Seq data may not be ideal for processed miRNA expression analysis for following reasons,

1. Some protocols use PolyA enriched RNA.
2. Most of the protocols involve size selection.
3. The precipitation step is different for mRNA and small RNA isolation.

With this background, use of RNA-Seq data for analysis of miRNA expression may produce inaccurate results.

Answer 2

[Buffo]

Shorts reads from RNA-seq are not miRNAs, you have to prepare special miRNA library.