Benjamin Callahan

One does what they can I suppose.

> #file paths > filtFs filtRs

@soluna1 If you used the same primer set and the same `trimLeft` parameters in each run, there should be no need for a `collapseNoMismatch` step. That function is mostly intended...

Awesome, thanks @dsamoht !

To double-check, when you run this code block without anything intervening. What do you get? Exact error messages and outputs. ``` table(file.exists(nopFw)) table(file.exists(nopRv)) out

On a brief glance, I would be a bit concerned about the small number of ASVs ("OTUs") that you are getting at the end of this. Can you tell us...

> I sequenced the mcra gene, coding for the Alpha subunit of the Methyl Com Reductase. The Primers were 1046f and 1435r. I used a corresponding reference database. So the...

> Many of my reads are very short... If that's the case, then it might just be unavoidable that you are losing most of your reads in the filtering step,...

Thanks @Lorze ! The semester is winding up, so I'll hopefully have a time to take a peek at this data in the next month or so. Download and format...

@luisymbio Since this is not being caused by dada2, but rather by the failed dependency RcppEigen, I would recommend trying the Bioconductor support site: https://support.bioconductor.org/ I don't have anything intelligent...