I would like to filter specific taxa from my table artifact and am unable to do so using
p-mode exact in the
qiime taxa filter-table command. I first use
--p-mode contains to remove Archaea and Eykaryota sequences in my filtered table and did not have technical issues:
qiime taxa filter-table\ --i-table table.qza \ --i-taxonomy taxonomy.qza \ --p-mode contains \ --p-exclude "D_0__Archaea","D_0__Eukaryota" \ --o-filtered-table filtered_domains.qza
I then remove specific taxa with
--p-mode exact using the output artifact as the input table
qiime taxa filter-table \ --i-table filtered_domains.qza \ --i-taxonomy taxonomy.qza \ --p-mode exact \ --p-exclude "D_0__Bacteria;D_1__Chloroflexi","D_0__Bacteria;D_1__Cyanobacteria" \ --o-filtered-table filtered_phyla.qza
When I use
filtered_phyla.qza as the input table for a taxa bar plot, I successfully removed Archaea and Eukaryota domains but failed to remove Chloroflexi and Cyanobacteria phylum from my dataset.
If anyone can address what I am doing wrong I would greatly appreciate it. I am currently using
qiime2-2020.2 if this information helps.