Trouble with LEfSe

Question

[PAnCakE]

Hi all, I would like to use my 16S community data from different mesocosms to create LEfSe graphs, but in the cladogram plots, I merely see a circle with yellow dots, no green, red and blue clades as in the LEfSe figures that I have seen in publications. Also, instead of taxa (like Pseudomonas or Bacillus), I see OTU identifiers, although they should be classified correctly. Can you tell me what I am doing wrong? Thanks, Boris

[PAnCakE]

Data as been prepared with mothur make.lefse command (on usegalaxy.eu), and further processing has been done on the galaxy server at Huttenhower lab.

Answer 1

[yiluheihei]

I'm developing a R package for microbiome marker discovery named microbiomeMarker, and the algorithm from lefse has been integrated to this package.

You can try it out today, if you want run lefse analysis in R. microbiomeMarker is still a newborn, While it’s not perfect.

Thanks. Any suggestions and contribution will be highly appreciated.