Using balance-taxonomy on collapsed taxa

[mortonjt (Jamie Morton)]

HI @biotama, it is also worthwhile pointing that if you collapse your biom table, the balance-taxonomy command is not expected to work with this format due to the taxonomy. I am not aware of a collapse taxonomy command just for the taxonomy.

Gneiss on collapsed FeatureTable

Hi @mortonjt, Collapsing beforehand would merge many singletons features into the same taxon labels thus eliminating the need to exclude them before running Gneiss. However, I still filter any remaining singletons features from the collapsed table afterwards. If the balance-taxonomy collapses internally why sometimes the same taxon can be found in both the numerator and denominator? Best, Ali