Hi, I installed lefse in my terminal by using the following command. conda install -c bioconda lefse I got following after installation. lefse2circlader.py lefse-plot_cladogram.py lefse-plot_res.py lefse-format_input.py lefse-plot_features.py lefty
I have my OTU table from Qiime2, and I used the relative abundance of OTU table. I followed instructions in the https://bitbucket.org/biobakery/biobakery/wiki/lefse page.
$ format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000 I used $lefse-format_input.py Saline_lefse.txt Saline_lefse.in -c 1 -s 2 -u 3 -o 1000000 But when I chekced ".in" file it doesnt seem the right output.
What do you think that might have gone wrong? I have attached my original OTU file, .in file and lefse error herewith for your reference. Any help is highly appreciated. Many thanks, Thilini