problems with cladogram plot

[Esther Merlini]

Hi everyone,

Do you know why I obtained the cladogram plot attached?

It seems like it is only half of it. Is there anything that i do not select? 

I have always used the platform, but now even if i upload DB that I used in the past it only generates that kind of plot.

thank you

Esther

[Jérémie Auger]

Not sure I understand the question. Your species list is longer than the number of dots on the cladogram?

This cladogram looks normal (with 6 levels of taxonomy; from kingdom down to species = 6). There doesn't seem to be much differences between groups though! (no colors).

I can have a look at your data table. I use it online (galaxy) and it won't ignore anything in the table once uploaded (it will bug before ignoring an extra line in my experience).

Have a great one, -JA 

[Esther Merlini]

thank you.

I have run the same DB few days ago and I obtained the cladogram I am now attaching.

Today, irrespective of the DB I uploaded, the program always generated the same plot. 

I tried DB from different studies, with different n of pts but the result is always the same.

I don't know why this is happening.

Esther

[Jérémie Auger]

What do you upload to LefSe? More than one table? 

I never uploaded my 16S bacterial DB to LefSe. The only table I import to LefSe is 'collapsed' (to use qiime2 terminology), meaning that the OTU (ASVs here) have been attributed to known species from the DB. Once the table with known species is done, no more need for a DB (and LefSe is doesn't accept bacterial DB). 

An example of such table's header is :

StoolType Cdifficile Cdifficile Normal Normal Cdifficile Cdifficile Cdifficile Normal Normal Normal     [....]

k__Bacteria|p__Actinobacteria|__|__|__|__ 0 0 0 0 0 0 0 0 0 0

k__Bacteria|p__Actinobacteria|c__Actinobacteria|__|__|__ 0 0 0 0 0 0 0 0.000136799 0.000146585 0

k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|__ 0 0.000203894 0 0 0 0 0 0 0 0.000160051

k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium 0.023879181 0.449892955 0.531491361 0.586286417 0.004139454 0.026031879 0.118603643 0.144186047 0.493623571 0.109101579

k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|__|__ 0 0 0 0 0 0 0 0.000273598 0 0

[....]

With more columns and more rows! But first line(s) is condition (and possibly subclass), one column per observation, and the lines are species. 

The shape of the cladogram is only determined by the list of species in the first column. 

Hope that clarifies things! 

Oh! And LefSe is a great tool to compare groups, spot the differences, but not to graph taxonomy alone. To see the species present in 1 experimental condition, Krona charts are much better (in my opinion). 

Have a great one, -JA