Question

miRNA from RNAseq data (Transcriptome)

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9.0 years ago

Mehmet ▴ 820

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 • 2.2k views

ADD COMMENT • link updated 22 months ago by Ram 43k • written 9.0 years ago by Mehmet ▴ 820

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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?

ADD REPLY • link updated 22 months ago by Ram 43k • written 8.6 years ago by kc.jeet • 0

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

ADD REPLY • link updated 22 months ago by Ram 43k • written 8.6 years ago by Devon Ryan 104k

score 1 · Answer 1 · 2015-04-05

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.