Odd display of demux plot

[Nicholas_Bokulich]

Hello again,
Thanks for digging up the issue associated with NovaSeq from the dada2 github page!

@kohlkopf

enforcing monotonicity in the fitted error model by changing the error model matrix.

QIIME 2 is just running a dada2 R script under the hood, so if you want to keep it all within QIIME 2 you could make a development branch of q2-dada2 and alter the R script to adjust the error model matrix inside that R script. Let me know if you want to go that route and have trouble locating the files that need to be modified and I can help you with that.

Otherwise it may just be simplest to process your data in dada2 directly in R, then import to QIIME 2 (see tutorial to do this below).

@benjjneb any other ideas? If this will become a common problem it might be neat to expose this functionality in q2-dada2.

Here is a tutorial for importing dada2 data from R into QIIME 2:

Importing dada2 and Phyloseq objects to QIIME 2

Importing dada2 and/or Phyloseq objects to QIIME 2 Background This tutorial describes how to take feature/OTU tables, taxonomy tables, and sample data (metadata) from R and import into QIIME 2. This might be useful if you have already completed analyses in R using (but probably not limited to) the dada2 and phyloseq packages and you want to add or compare to data analyzed in QIIME 2. You may also want to use or share data with the nice interactive visualization features of QIIME 2. This will hel…