RNA kinds expected in RNA-seq results

Kocur · 05-15-2013, 08:21 AM

Hi,

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,
Marcin.

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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05-15-2013, 08:21 AM	#1
Kocur Junior Member Location: Poznań, Poland Join Date: Mar 2013 Posts: 4	RNA kinds expected in RNA-seq results Hi, 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, Marcin.

05-22-2013, 06:46 AM	#2
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	It's pretty strange to find miRNAs because there are not polyA in their mature state (only poly-A in the pri-miRNA state)

05-22-2013, 03:38 PM	#3
rflrob Member Location: Berkeley, CA Join Date: May 2010 Posts: 50	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.

05-22-2013, 04:26 PM	#4
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	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.