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Old 12-09-2015, 05:35 PM   #5
luc
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Location: US

Join Date: Dec 2010
Posts: 466
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Hi GWOK, thanks for starting this thread!

We are experiencing the same problems (as is another lab in the neighborhood). The quality of the PE150 bp reads was perfectly fine a few months ago. Illumina likley has reagent quality problems at the moment.
The quality scores are now dropping considerably faster than a few months ago.
The % at which the median Q30 score curve ends (e.g. at cycle 310) seems to be a good quantifier for the problems. The curve used to end at about 60%, now often under 20%, even under 10%.

Illumina tech support did inform us that there are "NO reagent quality problems" - because all reagents individually pass QC. However they are investigating if there is a similar phenomenon ( a "non-problem"?) as with the MiSeq reagents which generate reduced read qualities scores since more than half a year now ( http://seqanswers.com/forums/showthread.php?t=59558 ).

Please keep us updated.

Last edited by luc; 12-09-2015 at 05:38 PM.
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