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miRNA from RNAseq data (Transcriptome)

Dear All

I would like to ask you whether I can get miRNA data from RNAseq (transcriptome) derived from Illumnia with pair-end reads. Does RNAseq data include miRNA?

Thanks.

rna-seq next-gen sequence
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updated by Ram Ram • written by Mehmet Mehmet

I have a question. How about transcriptome data with EST strategy? Can we do an in silico identification of miRNA by comparing the transcriptome sequence with the bknown miRNAs same as in case of identification of miRNA in EST sequence?

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updated by Ram Ram • written by kc.jeet • kc.jeet

The question wasn't about miRNA binding site prediction. Certainly one could do that from an assembled transcriptome.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

1 answer

You're unlikely to find much miRNA in a regular RNAseq run. There are typically size selections performed to get the right length of fragments loaded onto the flow cell, and miRNAs would be well below that size. Also, if polyA selection was performed then that would compound the deselection of miRNAs. That doesn't mean that there won't be any miRNAs, just not much. If you really want miRNAs, do a small RNAseq run.

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written by Devon Ryan Devon Ryan

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