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Make.lefse

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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.

Revisions

  • 1.32.0 - First Introduced
  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347