Hi 
I also questions about the input of LEfSe.
I’m using galaxy version of LEfSe. I’ve checked the example file of the input. In this file, it has the full taxonomy level of the otu table and the bacteria level is about to reach 1.
Bacteria
Bacteria|some_phylum1
Bacteria|some_phylum2
input file format link:
https://huttenhower.sph.harvard.edu/galaxy/root?tool_id=testtoolshed.g2.bx.psu.edu%2Frepos%2Fgeorge-weingart%2Flefse%2FLEfSe_for%2F1.0
Q1) Can I say that the Bacteria level is the sum of all other phylum belongs to Kingdom Bacteria? So in order to make this file, I need to calculate the abundance of each level for example, one file for phylum, one file for genera, one file for family et al. and then combine them together?
Q2) I also found that if I only give the full taxonomic name of some phylum see example below
Bacteria|phylum_1
Bacteria|phylum_2
I can also get result from LEfSe with three taxon levels: Bacteria, Bacteria|phylum_1, Bacteria|phylum_2. So I am wondering whether LEfSe will calculate the kingdom bacteria level within its script and produce the bacteria kingdom result? Even though it is not listed as a row for only Bacteria like in the example input.
Q3) What’s the differece between these 2? Which one I should use?
Q4) Single taxonomic level?
I also checked some blogs for single taxonomic level. How can I get lefse output for a single taxonomy level (e.g. species) only? - #4 by Kelsey_Thompson
In this blog, it says that the correct way is to replace “|” with “.” and only keep species level. Is that to change k_xx|p_xx|…|s__ → s__ ?
So I should use
s__sp1
s__sp2
as input format
But not k__xx|p_xx|…|s__ as input format?
I have searched many posts but I couldn’t find the answer. These three formats make me very confused, I appreciate any suggestions:).
Best Regards,
Lu