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Old 09-07-2015, 08:18 PM   #2
nucacidhunter
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Location: Melbourne

Join Date: Jan 2013
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In any PCR amplified library increasing sequencing depth will increase duplication rate as the diversity (# of unique fragments) is limited and sequencing more fragments will result in reads originating from the same initial fragment.
What you see is normal and I have seen around 10% dup rate using the same kit when around 40M reads/library was obtained. The rate was similar between bisulphite converted and non-converted libraries indicating the limits of kit and chemistry employed.
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