Hello ,
I am using LEfSe analysis for my data in UseGalaxy.org. The data is analyzed, but how could I plot the LEfSe results.
Thanks
Welcome, @chancat
At the UseGalaxy servers, LEFSe is bundled into the Mothur tools.
If you already processed the data for some of the upstream steps, you can still use the tools. You’ll need to format (actual file content) and label (format datatype) your data to match what the tools are expecting.
The full tutorial here covers each detail, and the shorter tutorial has some shortcuts with pre-processed data. These do not cover LEFSe directly, but maybe it provides some help anyway?
If that is what you have done already, and you are interested in generating graphics, your results are likely in a tabular format now. That means you can explore the tools under Visualize in the top menu. Or, you can start with a dataset in the history, and click on the visualize icon.
If you need to reformat your data, Galaxy hosts all of the regular command line utilities, and we have guides here that covers common choices. You can work with webtools from the tool panel, or go into an interactive environment and work in there. GTN Materials Search (Data Manipulation Olympics).
Hopefully this helps, and you can ask more followup questions. 