Cannot filter unassigned taxa: k__Bacteria;__;__;__;__;__;__

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1

My data are 16S amplicons (515F-806R primers), sequenced on Mi-Seq, processed by q2 with dada2 for QC, taxonomy by Greengenes 99%OTU database. Unfortunately, many amplicons are of host genomic DNA, according to NCBI Blast searches! These were assigned to the (level-7) taxon:

k__Bacteria;;;;;;

I am trying to use the feature-table filter to remove these based on taxonomy, but I cannot figure out what to enter for the --p-exclude parameter. I have tried:

–p-exclude “k__Bacteria;;;;;;”

yet, the filter fails to remove sequences with that taxonomic assignment. I think the issue is the syntax I am using, but I am not sure of the error I am making. I bet this is easy to solve, I just don’t know how… Any help would be much appreciated.

3

Hi @nvtravan,
In the taxonomic assignment, those underscores are not present (they only appear when you visualize these data, e.g., as a barplot or collapse a feature table on taxonomy).

See this post

So in your case you want something like this:

qiime feature-table filter-features \
  --i-table table.qza \
  --m-metadata-file taxonomy.qza \
  --p-where "Taxon='k__Bacteria' \
  --o-filtered-table filtered-table.qza

I hope that helps! Let me know if you’re still having trouble.

5

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