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Old 03-13-2017, 02:39 PM   #106
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Originally Posted by alexhaj View Post
Good work Brian! I am skeptical about your claim that NextSeq has less crossover than HiSeq or Miseq however.
We did fairly extensive analysis on this, and the results were never strongly reproducible from one run to the next on a given platform, but this one result (NextSeq outperforming HiSeq/MiSeq in crosstalk) was very consistent. Bearing in mind that we only had a single NextSeq machine at the time.

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Would you please provide some data to back this up.
I may try to dig it up if I have some time; there is no comprehensive single report with all of it so it would be a lot of work.

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And if that is the case maybe it's simply because demultiplexing is being done by CASAVA v2 on NextSeq and CASAVA v1 on HiSeq and Miseq. What if you did demultiplexing yourself, taking into account Quality scores (which I assume is not typically done).
I did do the demultiplexing manually, which is why (for example) mergebarcodes.sh and filterbarcodes.sh are in the BBTools package; I wrote them just for this experiment Even aggressive filtering on barcode quality was unable to substantially impact the relative differences between the platforms.
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