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Old 06-16-2015, 12:37 AM   #17
Location: Germany

Join Date: Jan 2013
Posts: 46

Originally Posted by pmiguel View Post
Actually that is pretty much what all 600 cycle runs seem to do. Oddly 500-550bp amplicons seems to PANDA merge just fine, so I tended to assume that the instrument was just losing its confidence. But since the phiX error rate also tends to sky rocket at this point, I am not sure what to think.

After talking to Illumina, they said it might be the library but they cannot exclude a failure of the reagents, so they sent new reagents. I went down from 1000 K/mm˛ to 700 K/mm˛ and increased PhiX from 5 % to 12 % and am now running the same library again. This costed me 8 M reads PF (down from 25 M to 17 M). I hope that it'll still be enough for the analysis.
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