We will be offering mothur and R workshops throughout 2019. Learn more.

List.otulabels

From mothur
Revision as of 15:45, 5 January 2017 by Westcott (Talk | contribs)

Jump to: navigation, search

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.otulabels commands.


Default Settings

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

mothur > list.otulabels(shared=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)


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