I’d like to filter specific OTU’s from my Feature Table a la Qiime 1 filter_otus_from_otu_table.py with -e. Ultimately, I am trying to remove a particular taxa at the order level. I have determined which taxa/OTU IDs are associated with this particular order and made a .tsv file with these IDs. Can I use the index-based filtering? If so, what should the header for the column be?
Hi @Diana_Williams! To exclude a set of features (e.g. OTUs) from your feature table based on feature ID you can use qiime feature-table filter-features with the new --p-exclude-ids option added in QIIME 2 2017.6.