Originally posted by gringer
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It shows that PCR-free libraries can hide a larger amount of adapters and adapter dimers somehow entangled in the y-adapters. We have several times seen surprises with (on the BA) clean looking PCR-free libraries in this regard.
Originally posted by gringer View Post1.5% index hopping with no adapters spiked in. Does that mean anything?
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Originally posted by ECO View PostAnyone doing significant multiplexing should be using dual indicies, which reduces this problem dramatically (making swapped reads go to Undetermined while demultiplexing).
Interested to see if this is a problem in our novaseq runs...will update if I note something.
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Originally posted by nucacidhunter View PostI wonder if there is any update on this.
Total output per lane was ~370-380M reads. With 8 i7 and 8 i5 indexes in each lane there are a total of 64 combinations possible, 8 expected combinations and 56 which may result from index hoping. I ran bcl2fastq (2.19.0) looking for all index pairs, permitting 1 mismatch per barcode.
For any given unexpected index pair produced through index hoping I found an average of ~35,000 (± 9,850) reads or approximately 0.01% of the total lane output.
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