filtering by taxa: SILVA


Im looking into the microbial diversity of the skin and I’ve used SILVA to classify my features.
Everything worked fine, but it turned out that in my data I have ASVs with taxonomy D_0__Bacteria;__

I’ve blasted those sequences and got a pretty nice match for mitochondria.

I’d like to filter those to proceed with alpha/beta diversity, but the problem is that ‘D_0__Bacteria;__’ is either not specific i.e.nothing gets filtered or too specific i.e. everything gets filtered and I end up having a table with only Eukaryota.
This is what I’ve used, with or without --p-mode
qiime taxa filter-table
–i-table biopsies_only_table.qza
–i-taxonomy taxonomy.qza
–p-exclude “D_0__Bacteria;;;;;;
–p-mode exact
–o-filtered-table biopsy_no_mt.qza

Question. is there the way I can go around this and get that specific taxa filtered?

Thank you very much!

Hi @Kotryna,

I have a couple of suggestions about the SILVA reference database.

  1. Update to the latest pre-made SILVA classifiers. If needed, you can train the classifiers yourself using these files.
  2. Use RESCRIPt to make your own SILVA reference database.

As for filtering away organelle / plastid sequences, see the documentation here.

Also, this information may help too.


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Hi @SoilRotifer,

thank you for you answer.
All information that you provide make sense, however the problem for me is the annotation of sequences to Bacteria… I have no problems filtering specific taxa or unassigned.
As in your example I have ASVs with Bacteria _ _ _ _ and if i filter for that, I get the empty table.
Havent worked with RESCRIPt before and will definitely look into that.



The last link I provided explains why you would not enter d__Bacteria;__;__;__;__;__;__, etc… for filtering.


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