Taxonomy assignment using bespoke weights on V3-V4

[Nicholas_Bokulich]

Hi @Ravenclaw,

@Ravenclaw

But my Illumina sequence data is from the V3-V4 region, and I don’t see that in Qiita.

You can use summarize-Qiita-metadata-category-and-contexts or query qiita directly using redbiom to see what "contexts" are available (this will detail the sequence domains available). It looks like there are several thousand V3-V5 samples present, and a smaller number of V3-V4. So you have a few options:

1. Use the V3-V5 samples from QIITA (if they are appropriate sample types), and train a V3-V5 classifier.
2. Use a custom collection of samples (e.g., from outside of Qiita) to assemble taxonomic weights.
3. Trim your reads to V4, though I agree that is a very unappealing option.

We are working on some solutions to make this easier in the future, e.g., use V4 class weights for any other domain, but right now it's complicated.

cc: @BenKaehler