DADA2 multiple runs with different number of samples

[Nicholas_Bokulich]

@RuneGronseth and @stangedal,
You are both correct in your assertions that dada2 should be run on each sequencing run/lane separately (absolutely do not combine runs prior to running dada2! )

@RuneGronseth

In the FMT-tutorial it says that " the DADA2 denoising process is only applicable to a single sequencing run at a time." Is that due to DADA2 itself, or is it related to how Qiime2 operates?

This is due to dada2 itself, not QIIME2. The error models assume that the data are from a single run, and differences in quality between runs upset this, potentially causing reads from a lower-quality run to be discarded.

@stangedal

I might have gotten this all wrong, but I thought we needed to upload the runs separately, run them through DADA2 separately, and merge the feature tables after this step because of the error model?

No, you are not wrong. You are absolutely correct.

@stangedal

I wonder if it matters that some runs contain many samples and others few when it comes to DADA2?

I believe that the number of samples does not matter at all — it is the number of reads that matters (but perhaps I am mistaken). I am not sure what guidelines there are on the minimum number of reads one should input to dada2, and perhaps @benjjneb can assist here.

I hope that helps!