feature-classifier extract-reads v3 v4

[colinbrislawn (Colin J Brislawn)]

Hello Linda,

Looks like we may be continuing the discussion started here.

Training classifier for taxonomic analysis

Hello Linda, This sounds like a great project! Have you tried using Greengenes2 with non-v4-16s, as shown in the main tutorial? EDIT: This does not make ASVs from your data like other pipelines. Instead, it directly compares your reads against the GG2 database entries, which already have a taxonomy. Simply counting database hits is also known as 'closed-ref-clustering'. This has very different tradeoffs than denoising -> taxonomy inference. While GG2 sh…

@Linda_Abenaim

What do you suggest for my region v3-v4?

Mehrbod and I both suggested the GreenGenes 2 database and qiime greengenes2 non-v4-16s, which does not require an 'extract-reads' step.

What's best for your data depends on what's in your data.

(If you included positive controls on your run with known composition, these can help you evaluate what methods work well.)

Try these out, see what works, and report back!