list.otulabels

The list.otulabels command lists otu labels from shared, relabund or list file. This list can be used especially with subsampled datasets when used with output from classify.otu, otu.association, or corr.axes to select specific otus using the get.otus or remove.otus commands.

Default Settings

The list.otulabels command reads a shared, relabund, list or constaxonomy file and creates a *.otulabels file.

mothur > list.otulabels(shared=final.an.0.03.subsample.0.03.pick.shared)

or

mothur > list.otulabels(relabund=final.an.0.03.subsample.0.03.pick.relabund)

or

mothur > list.otulabels(list=final.an.list)

or

mothur > list.otulabels(list=final.opti_mcc.0.03.constaxonomy)

If you open the final.an.0.03.subsample.0.03.pick.otulabels file you will see:

Otu001
Otu002
Otu003
Otu004
Otu005
Otu006
Otu007
Otu008
Otu009
Otu010
Otu011
Otu012
Otu013

Options

groups

The groups parameter allows you to specify which of the groups in your shared or relabund file you would like included. The groups option is ignored with the list file. The group names are separated by dashes.

label

The label parameter allows you to select what distance levels you would like, and are also separated by dashes.

Revisions

  • 1.26.0 - First Introduced
  • 1.30.0 - Added list file
  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347
  • 1.42.0 - Added constaxonomy file #581