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miRNA identification from RNA seq data

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

sequencing rna-seq next-gen mirna
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updated by Buffo Buffo • written by sa1987 • sa1987

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.

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written by Chirag Nepal Chirag Nepal

2 answers

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.

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written by Satyajeet Khare Satyajeet Khare

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

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written by Buffo Buffo

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