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HUMAnN3 and MetaPhlAn3 output analysis with MaAsLin2

Hi community ( @franzosa ) !!!
I have two groups of samples: case and control. I have output from MetaPhlAn3 and HUMAnN3. I want to find out the differentially abundant taxa in the control and case samples from the MetaPhlAn3 output and similarly, the differentially abundant pathways and gene families in the case and control groups from the HUMAnN3 output. Can I use MaAsLin2 for both purposes? If yes, can you please guide me?

Thanks for your time,
DC7

Hi!

You can absolutely use MaAsLin2 for the analysis of per feature differences from the MetaPhlAn and HUMAnN v3 output. There should be little to no difference in the background coding between using these feature tables and the one generated via v2. The tutorial is an excellent place to start to get a good idea of how to proceed: https://github.com/biobakery/biobakery/wiki/maaslin2

Best,
Kelsey

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