LEfSe after QIIME2 to test at all taxonomic levels

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Hi @MiriamGorostidi,

That's an excellent question! For general explanation on how to interpret things like __ and g__, I will link this previous, but clear answer from the forum: Follow-up on "'unique' taxonomy strings that seem to be shared" - #2 by Nicholas_Bokulich

The distinction is that the first row (ending in ; ) cannot be confidently classified beyond family level (probably because a close match does not exist in the reference database). So sequences receiving that classification can be any taxon in f__Geodermatophilaceae. The second row (ending in g__;s__) DOES have a close match in the reference database and hence is confidently classified at species level — unfortunately, that close match does not have genus or species-level annotations. This does not in any way imply that these two different taxonomic affiliations are related beyond the family level, so it would probably be inappropriate (or at least presumptuous) to collapse these at species level.

Now that we are (hopefully) on the same page with what those double underscores mean, what I ended up doing was updating my dokdo package to handle the double underscores better. For example, instead of outputting k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Intrasporangiaceae|f__Intrasporangiaceae|__, the 1.6.0-dev version now outputs k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Intrasporangiaceae|f__Intrasporangiaceae_x__L6. This way, if this particular taxon is returned as significant by LEfSe, it will show up as f__Intrasporangiaceae_x__L6 instead of __. For more examples, scroll up and click the files linked to my original tutorial; I updated those files. I will link one PDF file here as an example. output.pdf - Google Drive

Finally, if you wish to re-run your analysis with the 1.6.0-dev version of Dokdo, make sure to re-install Dokdo:

$ pip uninstall dokdo
$ git clone https://github.com/sbslee/dokdo
$ cd dokdo
$ git checkout 1.6.0-dev
$ pip install .

Hope this helps and let me know if you have any questions!

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