Benjamin Callahan

No it can't. DADA2 makes an assumption that there is a non-trivial fraction of error-free reads in the data, and that just isn't going to be the case with current...

Will need at least Q30 for DADA2/ASV approach to be appropriate for full length 16S.

I would stick with `maxEE=2`. In general, you don't want to tailor your filtering parameters to the outlier bad quality samples. Those often occur because of an issue in library...

Intuition is the same. Losing >90% reads at quality filtering step indicates a closer look.

> Would you think excluding samples with 60% loss is too conservative? I agree that it is a study-specific question without a one-size fits all threshold. That said, "excluding samples...

The description of the fasta file format for use with `assignTaxonomy` is here: https://benjjneb.github.io/dada2/training.html#formatting-custom-databases So if you can get the database into that format, then you are good to go....

Since `seqtab.nochim` is a matrix with rows corresponding to samples and columns corresponding to ASVs, the syntax you are using `seqtab.nochim[[i]]` isn't correct. Should be: `seqtab.nochim[i,]` to get the row...

You need to put the `uniquesToFasta` call inside the loop. Right now it is looping through each sample, and making a `seqvec` for each, but it doesn't output the fasta...

Let's start R side. Can you clarify the exact command you are running that leads to that R Session aborted error? Also, can you clarify how you are "running dada2...

In your R session, prior to running `removePrimers`, can you run the `sessionInfo()` command and post the output? The first thing I would look at is whether the list of...