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Old 01-18-2019, 01:18 AM   #9
Location: Aarhus, Denmark

Join Date: Mar 2008
Posts: 51

In our hands, we do not find any significant differences in the quality between insert data with perfect index reads and insert data with 1-mismatch index reads.
So despite a much larger fraction of 1-mismatch index reads the data is fine. Nice...

But it would be great with an explanation of how/why this index issue on the NovaSeq actually happen.
In our data, the issue is more frequent in index2 than in index1.
Can it have something to do with a more "loose" binding to the surface oligo when priming for reading index2? Or a sequence-specific higher (and systematic) error rate in index2 reading?
Any ideas?

And a list of indexes where one should expect a higher fraction of non-perfect indexes would be nice. Should we start one?
JakobHedegaard is offline   Reply With Quote