I tried to train the classifier using the Greengenes 13_8 99% OTU dataset for the 16S rRNA gene V3-V4 regions. I followed the tutorial "Training feature classifiers with q2-feature-classifier".
For the "extract-reads" command I did:
qiime feature-classifier extract-reads
After which I trained the Naive Bayes classifier.
Unfortunately, already in the "taxonomy.qzv" file (which I attach) many features stop at the domain.
I then applied the taxa barplot command to my filtered table and didn't get great results. Furthermore, there are no statistically significant differences regarding abundance at taxa level 6.
I'll explain my work to you: I'm trying to analyse the intestinal microbiome of an insect species raised on a control diet and a treated diet to understand if there are any differences of bacterial community.
Do you have suggestions for improving the analysis? The analysis of alpha and beta diversity was all significant.