Strange taxanomy based on Silva database

[SoilRotifer (Mike Robeson)]

You might be observing a propagated taxonomy? That is, any empty ranks are filled in with ranks from above. Reasons for this are described in the following threads:

SILVA 138 Classifiers

Hi @prince, To clarify, we do not curate the taxonomy, we are simply parsing the files as provided by SILVA. As for the upper-level taxonomy being propagated downward... this is intended by me. The reason for this is that not all reference sequences have taxonomic annotations for each rank. When a particular rank is missing, in this case the family level, the taxonomic rank above is propagated downward to a lower rank position until it finds a rank at a lower level, then it propagates that ran…

Weird Taxonomic classification 28S rRNA

Hi @HugoEira, welcome to ! I think you are one of the first to inform us about using RESCRIPt for SILVA LSU data! If you use your LSU classifier to classify your reads, and observe as the final classification that the upper level taxonomy is propagated downward through all of the ranks, then this means that you scored a hit to a specific sequence in the database that had no information other than 'Eukaryota'. That is, during the initial steps of constructing your database,…

-Cheers!
-Mike