make.lefse
The make.lefse command takes mothur’s shared file or relabund and creates a lefse formatted file. The LEfSe formatted file is can be used as an input to the LEfSe program. Segata, N., J. Izard, L. Waldron, D. Gevers, L. Miropolsky, W. S. Garrett, and C. Huttenhower. 2011. Metagenomic biomarker discovery and explanation. Genome Biol 12:R60
Default Setting
The make.lefse command requires a shared or relabund file.
mothur > make.lefse(shared=final.an.shared)
or
mothur > make.lefse(relabund=final.an.relabund)
If you open final.an.0.03.lefse, you will see:
group F003D000 F003D002 F003D004 F003D006 F003D008 ...
Otu001 0.075336 0.208835 0.203947 0.165535 0.067498 ...
Otu002 0.053969 0.109913 0.138816 0.130548 0.092043 ...
...
Options
design
design file with headers can be used to add more categories to your lefse file. NOTE: The lefse program will error when you format your data if you have more category lines than what can be assigned for class, subclass and id.
mothur > make.lefse(shared=final.an.shared, design=mouse.sex_time2.design)
If you open final.an.0.03.lefse, you will see:
age old old old2 young young ...
treatment F003Early F003Early F003Early F003Early F003Mid ...
group F003D000 F003D002 F003D004 F003D006 F003D008 ...
Otu001 0.0753362 0.208835 0.203947 0.165535 0.067498 ...
Otu002 0.0539694 0.109913 0.138816 0.130548 0.0920428 ...
Otu003 0.0760729 0.0391038 0.0949561 0.0823325 0.0635392 ...
...
constaxonomy
The constaxonomy parameter can be used to assign the OTUs classificaton instead of the OTULabel.
mothur > make.lefse(shared=final.an.shared, constaxonomy=final.an.0.03.cons.taxonomy)
If you open final.an.0.03.lefse, you will see:
group F003D000 F003D002 F003D004 F003D006 F003D008 ...
Bacteria_Otu001|"Bacteroidetes"_Otu001|"Bacteroidia"_Otu001|"Bacteroidales"_Otu001|"Porphyromonadaceae"_Otu001|unclassified 0.0753362 0.208835 0.203947 0.165535 0.067498 ...
Bacteria_Otu002|"Bacteroidetes"_Otu002|"Bacteroidia"_Otu002|"Bacteroidales"_Otu002|"Porphyromonadaceae"_Otu002|unclassified 0.0539694 0.109913 0.138816 0.130548 0.0920428 ...
...
groups
The groups parameter allows you to specify which of the groups in your shared file you would like included. The group names are separated by dashes.
mothur > make.lefse(shared=final.an.shared, groups=F003D000-F003D004)
scale
The scale parameter allows you to select what scale you would like to use to convert your shared file abundances to relative abundances. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.
label
The label parameter allows you to select what distance level you would like used, if none is given the first distance is used.