The bioBakery help forum

LEfSe cladogram problem

Hello,
I am trying to plot a cladogram of the results, and getting this image, which is missing all the information. Why is this happening?

Thank you,
Lena

Hi Lena,
It looks to me like the taxonomic structure of your data isn’t being read in correctly–double-check with the Input File Format section under the Galaxy Lefse tab “A) Format Data for LEfSe” to make sure your taxonomic labels match the correct format. Or, perhaps, does your data only include one taxonomic level (for instance, all features are listed only by their genus level)?
Best,
Meg

Hi Meg,
Thank you, I looked at the example file again, had to change ; to | and now it works.

However, now I have another question regarding results that appear as f___ or g___
I don’t see those in the results txt file, is it possible to change this presentation?

Thank you,
Lena

Hi Lena,
Sorry for the delayed response. I don’t know of a good way to change the presentation here, but the interpretation is that there are two different uncharacterized families in different parts of the cladogram that are each associated with the categorical outcome (one enriched in group 2, the other in group 1). You can manually change the labels if you want, to something like f__uncharacterized_XXX_Family , where XXX could be the name of the order the family is in. You’d have to do that in the .txt file, which should have some label at the family level whether it’s “f__” or “__”. Let me know if I can clear anything up!
Best,
Meg