So after looking online to try to figure out what is going on I decided to try qiime feature-table filter-features. Using this method worked, but if you could still tell me how to get the taxa filter-table, that would be great.
I do have an additional question for you, not sure if I should ask here, or create another string.
I will do the diversity metrics on the new table, and realized that I use the same rep-seqs.qza file created by DADA2 which is used for the phylogeny tree and downstream metrics. I saw your post here, which seems as if the unwanted samples will be dropped from the analysis, is this correct? If not, do I also have to filter the rep-seqs.qza prior to running phylogeny tree?