Ability to output DADA2 metrics

DADA2 has the ability to provide read counts across samples for each stage of processing. It would be very nice if QIIME2 could pass this information on. It’s a big time saver in identifying what went wrong when read counts are lower than expected (a question that has popped up multiple times here). Even when the counts look reasonable, I sometimes get asked for this information by a PI, which I currently can’t do without rerunning DADA2 outside of QIIME2.

The command for this is in the DAD2 tutuorial -https://benjjneb.github.io/dada2/tutorial.html

getN <- function(x) sum(getUniques(x))
track <- cbind(out, sapply(dadaFs, getN), sapply(mergers, getN), rowSums(seqtab), 
# If processing a single sample, remove the sapply calls: e.g. replace sapply(dadaFs, getN) with getN(dadaFs)
colnames(track) <- c("input", "filtered", "denoised", "merged", "tabled", "nonchim")
rownames(track) <- sample.names

Since we are a core facility that processes multiple projects from the same miseqs, it would also be nice to have the error profile plots for forward and reverse reads

plotErrors(errF, nominalQ=TRUE)


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Hey @Chris_Hemmerich!

You’re on the same wavelength as us, so to speak! We’ve already got an issue tracking this. I don’t know when it’ll happen for sure, but hopefully soon.


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QIIME 2 2017.12 is out now, and it includes more detailed logging when running DADA2!

I tried it out, and thanks - this is great!