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Old 01-18-2016, 11:06 AM   #16
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Location: Oklahoma

Join Date: Sep 2009
Posts: 411

Another run. Not as bad this time. Still not 2500-level good (for read 2) but not as terrible as before.

A few things we've learned thus far (empirically and from talking Illumina) regarding the 3k:

1) Anything short will take over the ordered flowcell with a vengeance. As best you can, DO NOT have library fragments <300bp (150bp insert). ALL adapter dimer must be gone. Do at least a 0.8x SPRI cleanup. This flowcell is much less forgiving than the 2500.

2) If you have libraries on the shorter side (200-300bp insert) it is better to OVER load than UNDER load.
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