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Old 10-12-2019, 05:25 PM   #1
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Location: Texas

Join Date: Jul 2019
Posts: 4
Default am I overclustered -- MiSeq

Hello, hope everybody had a good weekend so far. Sorry, I had a naive question and would appreciated it for any help.

I run a PE V2 run for MiSeq (cancer custom lib with Illlumina P7/P5 primer).
My target cluster density 1000-1200k, and I got 1328k, PF 95% and Q30 93%.

Although most of the Thumbnails seems OK (like #1), i did see lots of Thumbnails like #2 and #3 below. Will #2 suggest overclustered and #3 not focused Thumbnails? also, I could not explain why the base C has significant higher density than others (please see picture below) while I think my sample of high diversity. Am I overclusterd? Any explanation to help me understood these will be much appreciated.

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