Hi Nicholas,
Thank you for the reply.
I've run it with the pre-trained full-length 16S classifier(SILVA) and got a more satisfying result.
I moved on with the pre-trained one but still a bit bugged down with my V3V4 extracted classifiers because it gave exactly the same taxon for another set of data I have, for all 4802 feature IDs.
So I'm guessing there's something fishy with the classifier
I ran qiime taxa barplot and it is attached below:
taxa-bar-plots_prefiltered_ASQ.qzv (401.9 KB)
Looking at the barplot results, I've noticed another problem; the samples with the name "AJM" showed almost no variation in the taxonomy. The table.qzv file showed very low sequence depths for those samples.
It was difficult for me to understand why this is, because I've seen somewhat similar barplots for all samples when I ran it through qiime1:
Is such difference possibly coming from different properties of OTUs and ASVs?
Or is my table.qza file problematic?
Thanks,