make.biom

The make.biom command is design to allow you to convert your shared file to a biom file. To run this tutorial please download, example files

Default Settings

The shared parameter is required to run the make.biom command.

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

Options

constaxonomy

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

metadata

You can add sample data support (e.g., experimental factor, sample collection date, etc) using the metadata parameter.

For example if your metadata file looked like:

group  dpw description
F003D000   0   "F003D000 description"
F003D002   2   "F003D002 description"
F003D004   4   "F003D004 description"
F003D006   6       "F003D006 description"
F003D008   8       "F003D008 description"
F003D142   142     "F003D142 description"
F003D144   144     "F003D144 description"
F003D146   146     "F003D146 description"
F003D148   148     "F003D148 description"
F003D150   150     "F003D150 description"
MOCK.GQY1XT001 12  "MOCK.GQY1XT001 description"

Your biom file columns would look like:

"columns":[
           {"id":"F003D000", "metadata":{"dpw":"0", "description":"F003D000 description"}},
           {"id":"F003D002", "metadata":{"dpw":"2", "description":"F003D002 description"}},
           {"id":"F003D004", "metadata":{"dpw":"4", "description":"F003D004 description"}},
           {"id":"F003D006", "metadata":{"dpw":"6", "description":"F003D006 description"}},
           {"id":"F003D008", "metadata":{"dpw":"8", "description":"F003D008 description"}},
           {"id":"F003D142", "metadata":{"dpw":"142", "description":"F003D142 description"}},
           {"id":"F003D144", "metadata":{"dpw":"144", "description":"F003D144 description"}},
           {"id":"F003D146", "metadata":{"dpw":"146", "description":"F003D146 description"}},
           {"id":"F003D148", "metadata":{"dpw":"148", "description":"F003D148 description"}},
           {"id":"F003D150", "metadata":{"dpw":"150", "description":"F003D150 description"}},
           {"id":"MOCK.GQY1XT001", "metadata":{"dpw":"12", "description":"MOCK.GQY1XT001 description"}} ### output

The output parameter allows you to specify format of your biom file. Options hdf5 or simple. Default is hdf5, unless you are running a version without HDF5 libraries.

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

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.

picrust

The picrust program requires green genes OTU IDs. The picrust parameter allows you to provide the OTU ID mapping table associated with your reference taxonomy. When using the picrust option you must provide a reference taxonomy and a *.cons.taxonomy file. You can download the version 13.5 OTU ID maps here: GreenGenes Mapping Tables.

mothur > make.biom(shared=abrecovery.an.shared, label=0.03, reftaxonomy=gg_13_5_99.gg.tax, constaxonomy=abrecovery.an.0.03.cons.taxonomy, picrust=97.gg.otu_map)

mothur will create a biom file and a new shared file. The new shared file is created because picrust does not allow for duplicate OTU IDs, so any OTUs that are classified to the same taxonomy are merged.

reftaxonomy

The referencetax parameter is used with the picrust parameter. Picrust requires the greengenes OTU IDs to be in the biom file, and the referencetax parameter allows you to provide your reference taxonomy file you used when classifying your sequences.

Revisions