Erroneous taxonomy from Silva classifier

[SoilRotifer (Mike Robeson)]

Hi @marcelpolling,

@marcelpolling

The thing is that there is duplication in the taxonomic output

This is expected, as each unique feature is retained despite having identical taxonomy by default through our RESCRIPt plugin. As multiple sequence variants can derive from the same taxonomic group.

@marcelpolling

So from the 'class' onwards it is somehow giving the same result (Trebouxiophyceae or Ulvophyceae in this example). I wonder what is going on here.. I cannot really do any diversity analysis on this result, especially on the lowest hit, Cladophora vagabunda, where the genus is still showing the class Ulvophyceae.

When this taxonomic information is missing we propagate the taxonomic information, from the last observed upper-level taxonomic rank, downward. You can read more about why we do this within the RESCRIPt tutorial. Specifically, under the drop menu entitled Rank-Propagation.

In a nutshell, not all reference sequences within a given reference database contains complete taxonomic information. See the entry JX127171, for example. As you can see this entry only contains taxonomic information down to "Trebouxiophyceae". Thus, this label is propagated downward for all other ranks. Again, the paper and the tutorial linked above explain in far more detail why we do this. You can certainly disable rank-propagation if you'd like to make your own reference database with RESCRIPt.

Does this help?

-Mike