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Old 01-06-2010, 08:19 AM   #1
Location: US

Join Date: Feb 2008
Posts: 13
Default RNA SEQ Bias toward short transcripts (RPKM)

Hi there.
Just wanted to post this to see if anyone else see this interesting pattern. When taking the average expression (RPKMs) of short genes, say 0.5kb to 2.5kb, we see that the average is much higher when comparing to the average of longer genes, say 10.5-50.5kb. We have done a few wet lab work and were not able to find an answer to this pattern.

We have also took a few samples from the Mortazavi's data and were able to replicate the same pattern. This is telling us that for some reason, when looking at the entire RNA Seq run, we see a higher number of reads mapping to short transcript and lower number of reads mapping to longer transcript. The question is why? You expect to see similar averages, especially when you know that you are using the random primed protocol.

Do you see the same bias towards short transcripts in your RNA SEQ runs?
Thanks in advance.
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