The bioBakery help forum

How to add covariates for LEfSe analysis


I have one question about using Galaxy for lefse analysis.

I want to include two covariates and one group in the analysis, is the subclass category can be considered as one covariate (Select which row to use as subclass?)?

Tow covariates I want to include are continuous values.

Thanks in advance!

LEfSe isn’t designed to handle multiple/continuous covariates; for that I would recommend the tool MaAsLin2, which can adjust for any (reasonable) number of covariates of different types.
I hope that helps,