dada2 failed while running nextseq data

Technical Support
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Hello!
At least, there is some progress! I am sorry that it takes a long time to get it working.

Personally, I didn't find big differences by doing it with NextSeq data. So I am not sure if it will fix the issue, but maybe it will work in your case.

I would try the following:

  • Run Dada2 with F reads and increased "--p-min-fold-parent-over-abundance". Check post here.
  • Merge reads with vsearch and run Deblur
  • Use only F reads with Deblur

Best,

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