The bioBakery help forum

LefSe's example input file

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?

https://raw.githubusercontent.com/biobakery/biobakery/master/demos/biobakery_demos/data/lefse/input/hmp_small_aerobiosis.txt

Thanks,
Siyuan

Hi leahfa,

Thanks for the detailed info. I will have a try.