get.otus

The get.otus command selects otus from a given

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.

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.otus command selected the 598 otus from the accnos file.

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)

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)

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

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)