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Old 01-15-2019, 04:12 AM   #7
JakobHedegaard
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Location: Aarhus, Denmark

Join Date: Mar 2008
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And in a recent S2 (2x150) NovaSeq run of eight Nextera DNA Flex libraries prepared from human gDNA using indexes from the CD Indexes (96 Indexes, 96 Samples, cat# 20018708) we observed a single library with only 24-27% perfect reads. The index was from well F04, H701 (TAAGGCGA) + H522 (TTATGCGA) and the top non-perfect index was TAAGGCGA+TTTTGCGA (so a T in pos 3 in index2 where it should have been a A).
The other indexes in the run were find with a high fraction of perfect indexes.
Other observations of indexes with high fraction of non-perfect indexes?
We allow a single mismatch so we do get the data we need. We are though a bit worried that the quality may be affected.
And it would be great with an explanation of this index issue on the NovaSeq!
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