I can not find LefSe’s example input file: hmp_small_aerobiosis.txt. The original link on bioBakery can not be found. Does anyone has a clue?
No idea, but, I would suggest to you to run it directly on your own input file - lefse format is pretty straight forward. These are the important points:
-default is feature names in rows, sample names in columns
-EVERY column must have a header (you can name the feature column with “Group” or something like that
-you can input between 1 to 3 header rows (for class, subclass, sample ID - the last two are optional)
-headers can have only letters,digits or underscore . No special characters or spacers!
-If you want LEfSe to treat feature names as heirarchial - for example, run comparisons at species level, genus level, et cetera - use “|” to denote levels. For example: Bacteria|Firmicutes|Clostridia|Clostridiales|Lachnospiraceae|Blautia
This is also necessary if you want it to output a meaningful cladogram
Hi -
Were you having troubles accessing the following link?
https://bitbucket.org/biobakery/biobakery/raw/tip/demos/biobakery_demos/data/lefse/input/hmp_small_aerobiosis.txt
It worked okay for me. But we are going through a migration to GitHub so that might be causing issues. If the above link still does not work, could you try this new link at LefSe’s GitHub tutorial page?
Thanks,
Siyuan
Hello huttenhower lab team,
Thank you for your amazing tools and I am sorry to be unable to solve my issue through the previous discussions on the forum.
I am getting the following error
Traceback (most recent call last): File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 429, in class_sl,subclass_sl,class_hierarchy = get_class_slices(zip(*cls.values())) Fil
following is my input file.
Kindly help as soon as possible. Much thanks in anticipation.
–and
Hello,
Nothing strikes me as immediately wrong from the look of your input data, but I’m not able to tell what went wrong from the error message you saw. Can I get some more context of what command you ran that resulted in the error, as well as what version of LEfSe you’re using and from where? (Galaxy, PyPi, Conda, Docker?) I recommend using Galaxy or PyPi.
Thanks,
Meg
Thank you for your reply. I am using the galaxy version of LEfSe module. While I input this file on the LEfSe galaxy module I get the following error after input,
" Traceback (most recent call last): File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py ”, line 429, in class_sl,subclass_sl,class_hierarchy = get_class_slices(zip(*cls.values())) Fil