Benjamin Callahan

The number of reads corresponding to each ASV across the whole study is available by taking the `colSums` of the `seqtab`, since each column is a different ASV. So, to...

Hi Jake, I just wanted to say that your contribution here has not gone unnoticed. In fact it is highly appreciated, especially how you have not only contributed new data...

Hi Jake, We are digging into this in more detail in collaboration with a student here at NC State [@Y-Q-Si](https://github.com/Y-Q-Si) (email address [email protected]) who is interested in the error model...

Thanks @jonalim ! Pinging @Y-Q-Si

> BTW if there's interest in others getting the mock data to play with I could ask Jed if he'd mind us sharing Yes, if you have mock community data...

My first suggestions is to stop using `truncQ` to get rid of the artificial length variation that filtering technique introduces. It is almost never the right choice when analyzing data...

Hm, I see that there now. By default `truncQ=2` is enforced anyway by `filterAndTrim`, as several variations of Cassava/Illumina would start assigning Q=2 when it no longer had any idea...

If you are working at the ASV level, it is critical that you ensure that the exact same sequence region is covered by the ASVs in separate runs, especially when...

Have you seen our ITS tutorial workflow, in particular the section on identifying the presence of primers? https://benjjneb.github.io/dada2/ITS_workflow.html#identify-primers That should help. That said, often a visual inspection is sufficient, just...

The relevant data size for `learnErrors` is after doing filtering and trimming. What `filterAndTrim` command did you apply to the data? One option is to make filtering more stringent, which...