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Kocur 05-15-2013 08:21 AM

RNA kinds expected in RNA-seq results

We use RNA isolation and library preparation protocols which capture polyadenylated RNA. My question is what kinds of RNA can we expect to show up in results? At the moment, we get long non-coding RNAs, MIRs, SNORs, processed transcripts and pseudogenes. Is this to be expected?

Best regards,

NicoBxl 05-22-2013 06:46 AM

It's pretty strange to find miRNAs because there are not polyA in their mature state (only poly-A in the pri-miRNA state)

rflrob 05-22-2013 03:38 PM

We do find that we pick up reads that map to lots of these non-coding RNAs, but that they actually throw off the FPKM calculations quite a bit. I remove anything that I don't trust from my GTF file for cufflinks, and that improves the cross-sample reliability quite a bit.

Richard Finney 05-22-2013 04:26 PM

Careful, sometimes miRNAs are coincident with potential intronic segments of immature coding RNAs. Example : MIR26A2 "intronic" to CTDSP. Also, though the protocol maybe be "polya", other transcripts may show up. I don't know why, but it happens.

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