Hey, I encountered an issue: I was working on Galaxy and trying to run lefse but the output files were different when I changed the way microorganisms are named.
Here is everything that I know:
The dataset is green, the job did not fail.
The lef_usual.txt is a input file whose first column contained many names of microorganisms, and these names had some special characters like “()”, “-” and “'”, like “Clostridium_sp._DL-VIII”.
The lef_usual_result.svg is the output file. There are 5 biomarkers for “meNorChild”.
Then, I replaced all the names of microorganisms in the first column in lef_usual.txt with another way of naming, such as s1, s2 and s3. The new input file was named lef_number.txt.
The lef_number_result.svg is the new output file. There are 11 biomarkers for “meNorChild”.
The relevant parameters of the two tasks are the same, only the naming method of the first column of the input file has changed.
So, why does just changing the way microorganisms are named affect the final results? What format of naming will give the most correct results?
The process screenshots, input files and output files have been uploaded.
