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Old 07-24-2017, 12:28 PM   #104
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Originally Posted by pmiguel View Post
But I guess there is still the question of whether the index hop derives from a characteristic of the donor library, the recipient library or both?
We have several theories for what was driving this on HiSeq... the most plausible being something like, "library A had too many unincorporated adapters, library B had too many adapter-free inserts, and after mixing them, library B adopted some of the free adapters from library A". Which would indicate that it involves both the donor and recipient library. But I'm not sure if that mechanism is important for NovaSeq.

This seems like a really high rate of recombination, no?
Well, it's higher than what I observed for single-index libraries on our NovaSeq, but not by a huge amount.

Do you detect an increase in chimeric inserts? Depending on the mechanism of recombination you stipulate, there might be recombination events at any stretch of similar sequence, not just in the adapters.
I have not examined this on the NovaSeq yet, but I saw a much higher (several fold increase) of chimeric pairs when examining problematic reads on HiSeq. I don't remember the exact details; it might have been that reads mapped as improper pairs had a much higher rate of invalid barcode combinations, or vice-versa.[/QUOTE]
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