Filtering Unassigned Eukaryotes

[jecohen]

Hi! I've been using Qiime2 to visualize my data and recently analyzed it using the sequence database PR2. It worked well, but the barplot produced assigned some of the reads "Eukaryota;;". As I go down taxonomic levels, the number of spaces increases. Using Silva, those spaces will be marked with "p", "c", and other indicators of taxonomic levels. I'm having trouble filtering out these unassigned Eukaryotes without these phylogenetic determinates. Is there a way to filter these out? I've tried using "--p-mode exact" under qiime taxa filter-table but have not had success.
Thanks so much!

[Keegan-Evans]

@jecohen,

Those are simply features in your data for which the database itself does not have sufficient data to accurately assign a taxonomy at that level, but for which the tool can tell that you have enough information in your data to be able to assign to that level, if you had a relevant entry in Silva.

For an example of filtering based on taxonomy, check out this example in the Cancer Microbiome Intervention Tutorial. I do not think you will want to use --p-mode-exact. I think you will simply need to add a trailing semicolon to the query against the taxonomic annotation: `--p-exclude p__;.

As a warning, when you are filtering these out, you are disposing of good reads. Depending on how much data this filtering step eliminates, it might be worth trying to build a more specific or expanded reference database.

[jecohen]

Keegan,
Thanks for the quick response. I think I may have been unclear - the ";" indicators with this database are not given taxonomic labels and so they don't seem to be recognizable by Qiime's filters. Is there a way to identify these reads if they're not labeled "p_", "c_", etc?

Thanks!

[SoilRotifer (Mike Robeson)]

Hi @jecohen,

@jecohen

I think I may have been unclear - the ";" indicators with this database are not given taxonomic labels and so they don't seem to be recognizable by Qiime's filters.

The taxonomy prefixes (p__, c__, etc..) are removed to simplify the barplot visualization. If you'd like to view the actual taxonomy strings, along with the prefixes, you can make the following visualization as outlined in the PD mouse tutorial:

qiime metadata tabulate \
  --m-input-file ./taxonomy.qza \
  --o-visualization ./taxonomy.qzv

Then you can use the information there to guide your taxonomy filtering.

-Cheers!

[jecohen]

Thanks so much! I was able to get it