How to proceed in PICRUST2 after obtaining KO, EC and PAthabun?

[Shriya Sawant]

Hello,
I have obtained KO, EC and Pathabun data using QIIME2-Picrust2 plugin in .biom and .tsv format. How should I go about after this step in analysis of my data?
Please help.
Thankyou in advance.

[Gavin Douglas]

Hey there,

These data actually aren’t trivial to analyze - you can see my personal thoughts on them here: https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#how-should-i-analyze-the-picrust2-output

If you’re interested in differential abundance testing, I would suggest you try multiple approaches and make sure any inferences you make are robust to the choice of tool (i.e., that the functions that differ are identified by multiple DA tools).

You could also look at PCoAs, such as in the qiime2 tutorial on the plugin.

Last, STAMP is a useful tool for visualizing these datatypes, although I would not recommend relying on the statistical tests as they are not appropriate for compositional data.

Hopefully that helps,

Gavin

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