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Make.biom

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Revision as of 18:11, 23 April 2012 by Westcott (Talk | contribs) (Created page with 'The make.biom command is design to allow you to convert your shared file to a biom file. http://biom-format.org/documentation/biom_format.html To run this tutorial pleas...')

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The make.biom command is design to allow you to convert your shared file to a biom file. http://biom-format.org/documentation/biom_format.html To run this tutorial please download, Example Files


Default Settings

mothur > make.biom(shared=final.tx.1.subsample.1.pick.shared)

Options

contaxonomy

The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance. ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled.

mothur > make.biom(shared=final.tx.1.subsample.1.pick.shared, contaxonomy=final.tx.1.cons.taxonomy)


matrixtype

The matrixtype parameter allows you to select what type you would like to make. Choices are sparse and dense, default is sparse.

mothur > make.biom(shared=final.tx.1.subsample.1.pick.shared, matrixtype=dense)


groups

The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.

mothur > make.biom(shared=final.tx.1.subsample.1.pick.shared, groups=F003D000-F003D002-F003D008)

label

The label parameter allows you to select what distance levels you would like, and are also separated by dashes.


Revisions

  • 1.25.0 - First Introduced