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Old 05-15-2013, 08:21 AM   #1
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Location: Poznań, Poland

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Default 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?

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Old 05-22-2013, 06:46 AM   #2
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It's pretty strange to find miRNAs because there are not polyA in their mature state (only poly-A in the pri-miRNA state)
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Old 05-22-2013, 03:38 PM   #3
Location: Berkeley, CA

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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.
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Old 05-22-2013, 04:26 PM   #4
Richard Finney
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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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