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Difference between revisions of "Remove.otus"

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(Created page with 'The remove.otus command removes otus containing sequences from a specific group or set of groups. __TOC__ ==Default Settings== The group, list, label and either groups or a...')
 
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The [[remove.otus]] command removes otus containing sequences from a specific group or set of groups.  
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The remove.otus command removes otu labels from *.cons.taxonomy, *.corr.axes, *.otu.corr, shared and list files. This can be useful especially with subsampled datasets or when groups have been selected.
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__TOC__
 
__TOC__
  
==Default Settings==
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==Default Options==
The group, list, label and either groups or accnos are required. The command will generate a *.pick.* file.
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The remove.otus parameters are: constaxonomy, otucorr, corraxes, shared, list and accnos. The accnos parameter is required as well as at least one of the other file types.
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mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, corraxes=final.an.0.03.subsample.0.03.pick.pearson.corr.axes)
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This command will create a final.an.0.03.subsample.0.03.pick.pearson.corr.pick.axes containing the otus NOT in the accnos file.
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==Options==
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===constaxonomy===
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The constaxonomy parameter is used to input the results of the classify.otu command.
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mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, constaxonomy=final.an.0.03cons.taxonomy)
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The final.an.0.03cons.taxonomy contains 684 otus, but the remove.otulabels command selected the 86 otus NOT in the accnos file.
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===otucorr===
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The otucorr parameter is used to input the results of the otu.association command.
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mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, otucorr=final.an.0.03.subsample.0.03.pick.0.03.pearson.otu.corr)
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===corraxes===
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The corraxes parameter is used to input the results of the corr.axes command.
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mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, corraxes=final.an.0.03.subsample.0.03.pick.pearson.corr.axes)
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===list===
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The list parameter allows you to input a list file you wish to select OTUs from.
  
mothur > remove.otus(groups=B-C, group=esophagus.groups, 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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===shared===
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The shared parameter allows you to input a shared file you wish to select OTUs from.
  
mothur > remove.otus(accnos=esophagus.groups.accnos, group=esophagus.groups, list=esophagus.fn.list, label=0.03)
 
  
Both commands will output a new esophagus.fn.pick.0.03.list containing the 21 otus with no sequences in groups B or C, and well as esophagus.pick.0.03.groups.
 
  
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==Revisions==
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* 1.26.0 - First Introduced
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* 1.30.0 - Added list and shared parameters
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* 1.37.0 - Remove.otulabels name changed to remove.otus
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 15:04, 5 November 2015

The remove.otus command removes otu labels from *.cons.taxonomy, *.corr.axes, *.otu.corr, shared and list files. This can be useful especially with subsampled datasets or when groups have been selected.

Default Options

The remove.otus parameters are: constaxonomy, otucorr, corraxes, shared, list and accnos. The accnos parameter is required as well as at least one of the other file types.

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

This command will create a final.an.0.03.subsample.0.03.pick.pearson.corr.pick.axes containing the otus NOT in the accnos file.

Options

constaxonomy

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

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

The final.an.0.03cons.taxonomy contains 684 otus, but the remove.otulabels command selected the 86 otus NOT in the accnos file.

otucorr

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

mothur > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, 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 > remove.otus(accnos=final.an.0.03.subsample.0.03.pick.0.03.otus, 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.


Revisions

  • 1.26.0 - First Introduced
  • 1.30.0 - Added list and shared parameters
  • 1.37.0 - Remove.otulabels name changed to remove.otus