LEfSe input file problem



Hi all,

  1. I’m trying to run the LEfSe galaxy, and I made 2 different input files.
    All the data are exactly same, except for taxonomy name format.


However, the results of LEfSe from 2 different input files are totally different.


I don’t know which make input files make totally different results. Please explain it.

  1. I have one more question about the LEfSe input file.
    When I see the input format from the LEfSe website, it is not perfectly matched with relative abundance files
    It looks like the upper taxonomy category includes all the relative abundance in the lower taxonomy class.
    I want to make the same format input files, so is there anyone to teach me some command line to make LEfSe input file?