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Difference between revisions of "Get.otus"

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The [[get.otus]] command selects otus containing sequences from a specific group or set of groups.  
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The [[get.otus]] command selects otus from a given list.  
 
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==Default Settings==
 
==Default Settings==
The groups or accnos parameter is required. The command will generate a *.pick.* file.
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The accnos parameter is required. The command will generate a *.pick.* file.
  
  mothur > get.otus(groups=B-C, group=esophagus.groups, list=esophagus.fn.list, label=0.03)
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  mothur > get.otus(accnos=esophagus.groups.accnos, list=esophagus.fn.list, label=0.03)  
  
or you may wish to list your groups in a file instead of manually typing them. This can be done by using an accnos file.
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This command will output a new esophagus.fn.pick.0.03.list containing the 66 otus.
 
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mothur > get.otus(accnos=esophagus.groups.accnos, group=esophagus.groups, list=esophagus.fn.list, label=0.03)
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Both commands will output a new esophagus.fn.pick.0.03.list containing the 66 otus with sequences in groups B or C, and well as esophagus.pick.0.03.groups.
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==Options==
 
==Options==

Revision as of 15:56, 5 January 2017

The get.otus command selects otus from a given list.

Default Settings

The accnos parameter is required. The command will generate a *.pick.* file.

mothur > get.otus(accnos=esophagus.groups.accnos,  list=esophagus.fn.list, label=0.03) 

This command will output a new esophagus.fn.pick.0.03.list containing the 66 otus.

Options

constaxonomy

The constaxonomy parameter is used to input the results of the classify.otu command.

mothur > get.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otulabels, constaxonomy=final.an.0.03cons.taxonomy)

The final.an.0.03cons.taxonomy contains 684 otus, but the get.otulabels command selected the 598 otus from the accnos file.

otucorr

The otucorr parameter is used to input the results of the otu.association command.

mothur > get.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otulabels, otucorr=final.an.0.03.subsample.0.03.pick.0.03.pearson.otu.corr)


corraxes

The corraxes parameter is used to input the results of the corr.axes command.

mothur > get.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otulabels, corraxes=final.an.0.03.subsample.0.03.pick.pearson.corr.axes)

list

The list parameter allows you to input a list file you wish to select OTUs from.

shared

The shared parameter allows you to input a shared file you wish to select OTUs from.

mothur > get.otus(groups=B-C, shared=esophagus.fn.shared, label=0.03)

Revisions

  • 1.37.0 Merged functionality of get.otulabels command.