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Old 04-14-2012, 01:11 AM   #3
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
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I suspect that if you look at the per-sequence quality plots you'll see that this will be a subset of sequences with continually poor quality, and that a significant proportion of your library will be OK. If you look at the plots then the medians are OK on the second read, so it's a subset which is dragging down the lower quartile.

If you quality filter your data you'll probably have enough data left to continue your analysis.
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