Reverting to Qiime2 after using DADA2 in R

I have two MiSeq runs of 240 samples each that act as technical replicates. To analyse, I have denoised the runs separately, merged them, and finally removed chimeras all using DADA2 in RStudio (v1.14.0 and v1.2.5033 respectively). I first tried to do this with the dada2 plugin within qiime2 but merging the two runs proved difficult so I switched.

The output from the chimera removal is a single large matrix (8106720 elements, 36.7Mb), and I can’t work out how to save it in a format that I can then upload to qiime2 (v2019.4, linux cluster) for further clustering and taxonomic assignment.

I checked the formats and types that qiime2 can import (although I don’t understand the differences between types and formats, and can’t find documentation explaining them), and I don’t know how I could convert my matrix to fit. Is there a simple .rds to .qzv conversion?

The code I used is just the code in the big data tutorial so I won’t replicate it here.

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Hi @HollyJ,
There is a community tutorial describing this (not sure if it is out of date):

Good luck!

Hi Nicholas,

Thanks, but I’ve already looked at that tutorial and followed the relevant parts. I do not want to assign taxonomy in R, I want to do that step in the pipeline I already have in Qiime2.

That tutorial only shows how to make the feature tables, which I have done, but not the other artifact needed to complete the vsearch cluster step and feature-classifier classify-sklearn steps - the rep-seq part. Do you know how I can do that?

Thanks again,


Down at the bottom of that tutorial:

Let me know if that works!

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Oh… apparently I’m blind! Thank you so much!


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