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Old 06-06-2011, 11:45 AM   #5
JohnK@Genome_Quest
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Location: Worcester, MA

Join Date: Jun 2011
Posts: 7
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Quote:
Originally Posted by slny View Post
For mRNA Seq, if we remove the PCR duplicates, which actually occurred by random chance, then we will get wrong read counts. Is removal of PCR duplicates also recommended in mRNA Seq?
Also, I removed PCR duplicates for all applications- even RNA-Seq. Clearly, if you're trying to estimate transcript abundance, or estimate splicing-efficiency then PCR duplicates will have some sort of effect on your results. Now I'm not saying it'll be terrible, but subtle- yes. This of course is a matter of opinion, and I've seen people put up 'ok' arguments both ways. I'd say you'd have to get down into the finer details of your experiment as well as see how much PCR was done.
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