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
Question. is there the way I can go around this and get that specific taxa filtered?
Thank you very much!
I have a couple of suggestions about the SILVA reference database.
- Update to the latest pre-made SILVA classifiers. If needed, you can train the classifiers yourself using these files.
- 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.
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.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.