I tried to look for an answer for this question but found nothing similar-
I want to filter my rep-seqs.qza (after it was clustered and filtered along the table.qza) to 2 groups, based on the samples (in my example, I have 2 treatments (lettuce/tomato), with 3 samples each). How can I create 2 .qza files- one with the lettuce seqs and the other with the tomato seqs, that I can later convert to .fasta files and use for downstream applications?
I think the qiime feature-table filter-seqs will work great. You can run this command twice, once for lettuce and once for tomatoes, and change the --p-where flag. Like this: