I am trying to run LefSe analysis in Galaxy and I am having problems with the input file. I found the make.lefse tool in Galaxy and it requires the .shared, .constaxonomy and the experimental design file; I’m not sure what the experimental design should be like, anybody could give me an example so that I can adjust it to my own data?
I would suggest to make your own feature/otu/asv table outside of galaxy before starting Lefse analysis. In which case, you would have your OTUs as rows in the first column, and the samples for your class and subclass (if appropriate) as your first and second rows.
It is essentially a transposed shared file with the label column removed.
Let me know if you require more clarification.