Missing Features from merged dada2 Output

[benjjneb (Ben Callahan)]

@thermokarst

Unfortunately, I don’t think the strategy of running your samples through DADA2 one at a time will work as well as running them all at once

We don't recommend this as it is not as accurate, but it will probably work fine as long as individual samples are reasonably deep (>10k reads per sample).

@Micro_Biologist

However when I then try to run them through Vsearch OTU picking (denovo at 97%) it seems that there are more features in the sequence data than in the feature table. I have checked that all my samples are present in the feature table (as they are) and I have also checked the amount of features and there seems to be around 20 missing from the feature table, that are present in the sequence data.

I don't really understand what this means. It might be best to restate this a bit more precisely, perhaps by indicating the exsct commands that get you from "sequence data" to "feature table", and how you are tallying up the number of "features ... in the sequence data" vs. the number of "features... in the feature table".

One potential explanation, is that if you have run 97% OTU clustering on the output of DADA2, it will of course result in fewer features, because sequence variants that are 97% similar will be lumped into one OTU.