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Old 10-19-2011, 02:11 PM   #1
Location: San Diego

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Default RNASeq removing PCR bias

What is the best way to remove PCR bias in RNA-Seq? Is deleting all reads that map to the same start and stop position except the best quality read a good solution?
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Old 10-19-2011, 02:32 PM   #2
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The best way is to reduce the number of PCR cycles. Deleting "duplicate" reads is a very bad solution if you want do any kind of quantitative analysis. Here is a previous discussion on that topic:
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Old 10-20-2011, 03:47 PM   #3
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You should check this post. Its one of the best discussions I have read.

Especially replies by malachig, kmcarr and lh3.
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Old 10-20-2011, 07:00 PM   #4
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Fragment duplication is just one kind of PCR bias. Base content is another.
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