Why denoising itself on DADA2 is filtering some reads?

Hi,
I was taking a look on this reply by @FrancineMarques and now I am wondering why reads are being filtered on denoising step from DADA2? (“denoised” columns from stats file)

As far as I know, this did not happen in early implementations of qiime dada2 plugin (am I right?)

Thank you

Hi @vheidrich!

Have you had a chance to read the DADA2 paper?

Not all reads are able to be denoised (for reasons discussed in the paper above), which is why the step might indicate a decrease in read count.

No, I think that has been the case for as long as this plugin has existed (someone please correct me if I am wrong). The denoising summary is a bit newer than the plugin itself, though, but I think it is 2 or 3 years old now at this point.

:qiime2:

Hi @thermokarst! Thank you very much for your reply

Some days ago, after some detective work, I found the answer for my question in another place. Apparently, there wasn’t read loss in denoising step in earlier dada2 versions, including the one implemented in qiime2-2019.1. Since dada2 version 1.8, a quite irrelevant number of reads might be excluded during denoising.

Previous behavior (“correct everything”) can be recovered in R implementation of dada2. I am afraid we can’t force current QIIME2 implementation of dada2 to “correct everything”, right?

Thanks again

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