Benjamin Callahan

The way you have written the species names, every species is being considered as distinct. The text parser reads `acnes_A1` and `acnes_A10` as two difference species. You didn't state what...

Hi Alejandro, Glad that the package has been useful for you! For taxonomic assignment in DADA2, you should take a look at the taxonomic references page: https://benjjneb.github.io/dada2/training.html The reference fasta...

> Although the program needs a 100% match between the sequences to be assigned, right? It is a bit stringent with my current databases, if this is correct. For example,...

Depends on your study goals. I would recommend just not calculating richness at all, for the reasons discussed in that paper. If you want to look at alpha-diversity, the Shannon...

Chimera removal and singletons cannot eliminate many of the types of artefacts they talk about in the paper, like cross-contamination between samples. That said, enforcing a minimum abundance threshold necessarily...

I'd try to find out what the primers were. I suppose you can try to reverse-engineer it. BLAST some sequences to figure out if its ITS1 or ITS2 or something,...

You can put the taxonomy assignments together with the sequence table using `cbind`, i.e. column bind, in R: ``` df.combined

First, it might be useful to take a look at #565 for a look at what some other people have been looking at with regards to variable length merging, and...

> Is there a reason for each plot going up to either 15 or 2 mismatches? Yes, see this block of code from the `mergePairs` function: ``` if(maxMismatch==0) { setDadaOpt(MATCH=1L,...

The first thing I'm seeing is that the primer counts are "symmetric" between the ForwardReads and ReverseReads before running cutadapt. That is, there are just as many hits of e.g....