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Old 06-06-2011, 03:37 PM   #6
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Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319

If you have paired-end data for RNA-seq, PCR duplicates should be removed. There is a very low probability to get identically mapping paired-end reads and the bias from leaving PCR duplicates will almost certainly be worse than the removal of a few genuine fragments.
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