LEfSe after QIIME2 to test at all taxonomic levels

Hi @yxa,

I just wanted to extend @gregcaporaso's comment, with a few additional options:

  1. Use qiime rescript edit-taxonomy ... to remove everything but the genus ranks. You can enable the --p-use-regex flag to make this easier. Then you can feed this output into the dokdo prepare-lefse ... command

  2. Or after you run dokdo prepare-lefse..., open the resulting text file. You'll see that LEfSe delimits that taxonomic ranks with a | character. You can simply find and replace all of the | with . or _ characters so that that taxonomy is simply one long string. You can feed this into LEfSe for analyses. Note the taxonomic cladogram will not be informative, as it'll look like a "star" w/o hierarchy. Or remove as many of these delimiters you'd like up to the rank you want to focus on, then run LEfSe.