Hi!
I have a problem importing my data to use LEfSe. The file is a tab separated txt file.
It won’t let me choose a class row. There is nothing popping up if I click the balk with ‘Choose an option’. Is this an error or do I have to prep my file in a different way?
With kind regards,
Eva!
Which Galaxy are you using? The LEfSe seems only support Python 2.
Thanks for your reply!
I’m using the online tool. The file was prepped in R, exported to excel, and then saved as tab delimited txt file.
The example file given at the online tool does work, however. Also if I copy paste in into excel and safe it as tab delimited txt file, so this does not seem to be the problem.
Hi everyone,
I am also using the online tool of Lefse and coming across the same issue. I have the input as an excel file and saved it as a text (tab delimited file), and still coming across the same problem. I cannot access the class or sub-class.
Please help with this issue.
Thank you
Vijay
Hi, all!
I had the same issue when using the online tool of LEfSe and I could not choose the class option as well.
In my case, I prepared the txt file from qiime2 output to LEfSe format text file in LibreOffice and then
tried to solve this problem with Python 2.7, but I got the error message as below.
“if r[0] in [‘0’,‘1’,‘2’,‘3’,‘4’,‘5’,‘6’,‘7’,‘8’,‘9’,’_’]: indexerror: string index out of range”
So, I made the tab delimited text file (.tsv) with the other program, Excel in MS Office.
Surprisingly, the file did work well in both online LEfSe and python 2.7, and the class and subclass were identified in LEfSe system.
I did not find the differences between the txt file from LibreOffice and from Excel, but I think if you change some values (ex, round up) or prepare the new text file again in a different way, you could analyze your data like my case.
Hope you can solve this problem.
with Best regards,
Hyo-JIn
Hi, Hyo! Thanks for your gentle report. Can you, please, share with us the .txt file you used in Galaxy. The succesfull one, by the way
Best,
André
