How to extract taxon name unique

General Discussion
1

Hello everyone,

I am struggling with a problem I would like to solve inside the qiime2 eviroment. I am running an experiment in which I have two groups that have different alpha diversity for the observed features metric. I would like to visualize (maybe a qzv) what are the taxon name of the features that are present in a group and not in the other. Is that possible?
I usually use the consensus blast to classify.

Thanks in advance,
Federico

2

Hello!
It is not possible to perform it in qiime2 without doing some tasks outside.
I will try to provide you with possible steps.

  1. Classify your reads.

You can use this method or any other that suits you.

  1. Collapse your feature table to desired tyxonomy level, for example, genus.

  2. Split your feature table on groups you are comparing for alpha diversity.

  3. Either visualize your split and collapsed tables to get a list of taxa present, or (better!) run core-features plugin to get list of core-features at the appropriate threshold.

  4. Create a Venn diagram (for up to 4 groups) or UpSet plot (for more than 4 groups) outside of qiime2. For Venn diagrams, you can use the online tool interactivenn.

PS. If you are a Python guy, please check my package Venny4py for Venn diagrams (up to 4), which will create a figure plus txt file with unique features for each group/combination of groups.

Best,
Timur

1 Like
3

Thanks a lot @timanix!

I usually do this step on Excel after collapsing and exporting the feature table but I was wondering if it was possible to do that on qiime2. Anyway I'm gonna try to use your method now, very thank you for responding so quickly, it was very helpful, even just to know that it wasn't possible to do it on Qiime2.

Best,
Federico