I just started using qiime2 for a project where I have data from two 16S regions as well as 18S. I've been following the advice to build custom classifiers for each region, based on the amplification primers. However, so far the "best" results have come from the full GreenGenes dataset without refin…

Thanks @aphanotus for your questions. Are you setting the --p-confidence parameter when you run qiime feature-classifier classify? If not, then if OTUs are not being named at low taxonomic levels then I suspect it is because they may be being assigned labels from the reference taxonomy that don't …

@BenKaehler , could you answer this question?

[image] aphanotus: What are the relative merits of classification with GreenGenes vs. SILVA? This is a good question. The Greengenes taxonomy is a bit easier to work with computationally, as the taxonomy strings are more concise and the taxonomic levels are more consistent. In Greengenes ther…

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Classification using GreenGenes v. SILVA

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