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Old 06-06-2011, 11:09 AM   #4
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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?
Essentially, you're removing them because you can't disambiguate whether the read came from a unique bead source versus PCR. IMO, I removed PCR dups based on start and stop alone, because PCR has an inherent error rate. As before, you can't tell whether the base-differences (mm) came from independent events, or PCR-error.
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