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Old 06-10-2015, 04:03 PM   #15
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Location: Monash University, Melbourne, Australia.

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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.
I have had the same experience...

The quality seems to drop quite badly. For us, it's often about half way through the read. But, our libraries on 2x300b runs are almost always low diversity so I have often thought (but not yet rigorously tested) that this was a contributing factor. The apparent error rate from (from the PhiX spike-in) seems to be high, too... but, as you mentioned, the R1 and R2 reads (i.e. per cluster) assemble to each other very well.

We have been told discretely by Illumina staff that there is an diagnosed issue with some 600c kits and that we should keep an eye on the progress, and report any problems with loss of quality in the second read.

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