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

Difference between revisions of "Get.otus"

From mothur
Jump to: navigation, search
(Created page with 'The get.otus command selects otus containing sequences from a specific group or set of groups. __TOC__ ==Default Settings== The group, list, label and either groups or accn...')
 
(Revisions)
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
The [[get.otus]] command selects otus containing sequences from a specific group or set of groups.  
+
The [[get.otus]] command selects otus from a given list.  
 
__TOC__
 
__TOC__
  
 
==Default Settings==
 
==Default Settings==
The group, list, label and either groups or accnos are required. The command will generate a *.pick.* file.
+
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)
+
  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.
+
This command will output a new esophagus.fn.pick.0.03.list containing the 66 otus.
  
mothur > get.otus(accnos=esophagus.groups.accnos, group=esophagus.groups, list=esophagus.fn.list, label=0.03)
+
==Options==
 +
===constaxonomy===
 +
The constaxonomy parameter is used to input the results of the classify.otu command.
  
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.
+
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.
 +
* 1.40.0 - Speed and memory improvements for shared files. [https://github.com/mothur/mothur/issues/357 #357] , [https://github.com/mothur/mothur/issues/347 #347]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 14:16, 29 March 2018

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