Import RDP classifier output taxonomy file into qiime2

[SoilRotifer (Mike Robeson)]

Use --p-exclude Archaea Eukaryota.

However, I'd advise against removing these groups, as you'll want to keep off-target / outgroup taxa in your database. Otherwise you'll likely identify many taxa incorrectly as "d__Bacteria; ;", when in fact they may be Archaea or Eukaryota.

See:

Rescript Plugin for 18S

Hi @lmjackson, welcome to ! Can you provide details on which primer set you used to generate your sequence data? Many primer sets will amplify off-target sequences. That is just the nature of the process. How much of your sequence data is being returned as Bacterial? Few? Many? I would advise against removing removing groups of taxa just because your are unable to identify what you want. In fact, it is best to leave these "outgroup" taxa within your database. This way you can more c…

Greengenes Versus Silva

Hi @Tiago_Bruno_Rezende, welcome to ! Great question! The reason that the SILVA alignment uses Uracils instead of Thymines, is because the curated sequence alignment is informed by secondary structure in order to reduce alignment ambiguity. So, we honor the reality of the rRNA molecule when using this secondary structure information to inform our alignment. Also, it is easy enough to simple replace these when needed. Nope. Though I am sure you can find files generated by thir…