I have identified species that characterize the differences between cases and controls in my study.
There were several taxa that had LDA>2 (lefSe.pdf)
When I generated the accompanying cladogram (cladogramm.pdf),
some of the top species were absent in it.
For example, ‘Eubacterium_sp_CAG_180’ and ‘Prevotella_sp_AM42_24’ were absent in the cladogram.
I also checked to see if they were represented at the genus level or any higher-level branch of the phylogeny that can include them. The cladogram had no such higher-level taxa.
Can you, please, help me with this issue?
What I believe is happening here is that LEfSe’s default is to only plot six taxonomic levels (to the genus level) if you change that to seven levels that may solve the issue. On the galaxy site go to Set structural parameters of the cladogram → Advanced → Then change Maximum number of taxonomic levels to 7.
If that doesn’t work, you can always pull the data and custom map it using the GraPhlAn tool, which is what underlies the LEfSe cladogram function but has a lot more customization.
I hope this helps!
It worked. Thanks a lot for your help with this!