The bioBakery help forum parameters: how do they affect the pipeline and the plots?

Hello everyone,

I am trying to analyse some data with LEfSe on anaconda (python).
I successfully execute the script with the example data


Is the cladogram supposed to look like this? If so, how can I change the colors for the biomarkers? If not, I believe it is because no biomarker clade was found (I could not generate the other picture (step 3, see below)).

The code I run is the following:

bin/ tmp/sample.txt tmp/merged_abundance_table.lefse
bin/ tmp/merged_abundance_table.lefse tmp/merged_abundance_table.lefse.out -l 4
bin/ --dpi 300 tmp/merged_abundance_table.lefse.out output_images/lefse_biomarkers.png
bin/ --dpi 300 tmp/merged_abundance_table.lefse.out tmp/lefse_biomarkers.png

I am not sure about the parameters (-c,-s,-u,-o) what do they do? Online I could not find any info and the code where they are used is not commented so, before trying to back-engineer everything I am glad to ask.



Hi Pietro,

Thanks for the question! The cladogram you produced does look correct if there were no significant features to plot on it.

As for the parameters:
-c = row of the data to use as the class
-s = row that contains the subclass information
-u = the row with the subject information
-o = the normalization (for LEfSe the default is [1.0] or none)

I have attached the help page for the format LEfSe step. I hope this helps. Let us know if we can do anything else.


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