Hello, I'm running a singal read dual indexed library on NextSeq, with a custom primer for index 2. While my general run metrics looked fine (clustering and pass filter rates ok) and my Read 1 Q30 was great (91%), both of my index reads crashed out with Q30 values in the 60s. Looking at the flowcell %>Q30 on SAV, once we hit the index reads most of the tiles start coming up grey. Obviously, we didn't get many reads assigned to samples, but I've never seen this before. Any ideas on why this happened, and how to remedy in the future?
Thanks!
Thanks!
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