I am working on trying to filter out taxa with no identifiers (i.e., ;;) from my FeatureData[Frequency] tables and, then collapsing them to a taxonomic level using the qiime taxa collapse command.
I have been using the following command for filtering:
qiime taxa filter-table
To my understanding, this should keep all taxa resolved to D_5__ (genus) and which contains a taxonomic name, but discard any taxa that contained unassigned taxa down to a genus level (i.e. D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Corynebacteriales;; should be removed).
I am then attempting to collapse my filtered table to a genus level using the following command:
qiime taxa collapse --i-table table2.qza --i-taxonomy taxonomy.qza --p-level 6 --o-collapsed-table genus_table.qza
Both commands run fine and produce FeatureData[Frequency] tables, though still contain unassigned taxa.
Now that I write this out, is this a case where using the *qiime feature-table filter-features" command might work on the collapsed table? I cannot use the qiime taxa filter command on the collapsed table because the “ASVs”/Features are no longer hash codes but taxonomic lineages. Is there an easy way to use the “–p-where” command that would allow me to filter out unassigned taxa in my collapse table?
I’ll leave this here while I go try it out myself, but any suggestions would be greatly appreciated (particularly if there is some flaw in my code/method above).