I have two problems:
- 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?
There are some bacteria (genus level) found in both the negative controls and in the actual samples. I am not sure how to handle this contamination problem.
I have read in previous studies, that you can use a filtration script in QIIME to do this. Can you please guide me how to perform this step?
- 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 %?
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.
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!
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