I was wondering if there is a way to filter your representative sequences or taxonomy file to exclude chloroplast and mitochondria sequences. I have filtered my feature table, but now my taxonomy and filter table do not match. Can you suggest a way to limit my rep-seqs or tax file to be the same as my filtered feature table?
Hi @vogelm! Have you had a chance to check out the Filtering Tutorial? We added a new section to that tutorial (plus some new methods to go with it) in QIIME 2 2017.10 that covers your use case. Let us know how it goes!
