Hi I have a question on the missing phyla/genera in the taxa-bar-plot.csv file. I wanted to see if my data contains Akkermansia under phyla Verrucomicrobia, but I saw that Akkermansia as well as Verrucomicrobia are not present in my data that I downloaded from the taxa-bar-plot. Does this simply mean that my samples contain zero Verrucomicrobia?
I used Naive Bayes classifier trained on 99% Greengenes that I downloaded from Qiime, and it should include Verrucomicrobia phyla.
There are two approaches I can recomend:
Try the SILVA v138 classifiers.
If you need to you can make the classifiers yourself using these files. If you are using an alternate amplicon region, checkout RESCRIPt to make your own SILVA reference files.
Sanity check that your taxa are present, or not.
An easier way to search through your taxonomy would be to tabulate the taxonomy file into a visualizer, like so:
qiime metadata tabulate \
--m-input-file taxonomy.qza \
Enter in “Verrucomicrobia” or “Akkermansia” into the search field in the visualizer. This will list the features with that taxonomy.
Then you can visually inspect your feature-table for these features through the feature-table visualizer. If you’ve not done so already, you can run:
qiime feature-table summarize \
--i-table table.qza \
--o-visualization table.qzv \
Then click on the
Feature Detail tab of the
table.qzv and use your web browser’s
Find function to search for that feature. Then you’ll get a good idea of how many reads and samples in which that feature is present.
This is simply more thorough way of making sure certain taxa are or are not present.
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