The bioBakery help forum

Trying to run output from FAPROTAX

I am trying to run lefse on my output from FAPROTAX but it isnt running. Wondering if anyone has done this before and could be of help. I have attached the data i am inputting LEFSE.txt (58.0 KB)

Thanks for your question. It looks like you have only one sample per value of the “Description” variable, so none of your tests are showing up as significant (the test is for statistical significance, and that can’t be assessed with only one sample per group). If you can simplify the Description variable into a Case/Control or Control/Treatment1/Treatment2, etc., that should help, although you still have a relatively small sample size, so you might not see differences. Just to clarify, does each column in your data represent a single sample, or is FAPROTAX output a summary across multiple samples in each group? LEfSe needs the sample-level data in order to work properly.

Thank you so much for your response. I’ll revisit my input data and try again