Issue using Silva classifier high number of only Bacteria assigned

[SoilRotifer (Mike Robeson)]

Hi @geryale29,

The likely cause if the fact that many of your sequences are not in the same 5' - 3' orientation as the reference classifier. That is, they are in a mixed orientation, as discussed in quite a few threads.

I refer you to the following threads, as a potential way to get your sequences oriented:

• bullet list / sanity checks
• classifier for forward reads
• preparing mixed orientation reads for dada 2