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.