How can I use "Filtering data tutorial" to substract found bacteria in the negative controls from the samples (taxa-bar-plot) and only visualize the most common genera?

[Nicholas_Bokulich]

Hi @Jasmine84,

@Jasmine84

I want to see what is left of my classified bacteria when I remove bacteria in my negative controls as they are contamination. How can I substract the bacteria found in my negative controls from the bacteria in the actual samples?

we have discussed this topic a lot on the forum, e.g., here — it is a bit risky to decide that anything detected in a negative control is contamination (as opposed to cross-contamination from real samples). I would advise you to proceed with caution unless if these are obvious contaminants.

You can filter specific taxa from a feature table or from sequence artifacts as described in this tutorial.

@Jasmine84

How can I sort my taxa bar plot so that only the most 20 abundant genera is shown? Or sort the taxa with only including the bacteria present more than for example 1 %?

You will need to use feature-table filter-features to filter the feature table before constructing a taxonomy barplot.

We do have an open issue to support interactive filtering from within a barplot, but I am not sure there are any plans to implement this in the near future...

I hope that helps!