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Old 01-04-2016, 05:30 AM   #10
GW_OK
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Location: Oklahoma

Join Date: Sep 2009
Posts: 411
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Update.
After running a mix of PhiX and other libraries Q30 plots are still not great but perhaps less terrible. Attached here are two plots showing a PhiX lane as well as a Nextera lane (PhiX is missing one of the two index reads).

While neither are bottoming out as before there's certainly a steep downward trend in read after the intensity jump. This run did "meet spec" for a 3k run (75% >Q30) but Illumina still wants to send out an "instrument expert" to have a look at our machine.
Attached Images
File Type: png Screen Shot 2016-01-04 at 8.19.53 AM.png (54.2 KB, 14 views)
File Type: png Screen Shot 2016-01-04 at 8.20.34 AM.png (55.9 KB, 13 views)
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