filtering features for top genera and exclusive features

Hi Qiime community,

I was hoping to get some help creating a heatmap (qiime feature-table heatmap) that only contains the top 50 genera (abundance). I have successfully used qiime taxa collapse to create a collapsed table for genera data, but the corresponding heatmap is too long :sweat_smile:. Thus, I was hoping there would be a way to filter the features to show only the top genera.

In addition, I have 2 groups for comparison and would like to know if I could filter features to create a table that shows features that are present in all replicates for one group (exclusive to that one group) but not the other group. It would be really useful to compare which features are exclusive to each group.

Thank you for all your help! :slight_smile:

Hi @jng!
Have you played with qiime feature-table filter-features? The filtering tutorial, especially the metadata filtering section and the docs linked above will give you some basic background.

It’s a powerful tool, so there are a number of different approaches you might take. I haven’t tested any of the following for your specific situation, but they represent a few possible approaches.

For your first question, --p-min-frequency could probably be used, by passing the number of features in the 50th-most-prevalent feature. This is probably not the best approach, but would do the job.

For your second question, you might be able to filter tables to include all features in each group, then pass these tables as metadata, using --p-exclude-ids to remove any overlapping (non-exclusive) features.

Good luck!
Chris

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Thank you @ChrisKeefe!!

I followed your suggestions and it worked perfectly :slightly_smiling_face:

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