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

Difference between revisions of "Make.biom"

From mothur
Jump to: navigation, search
 
(One intermediate revision by the same user not shown)
Line 10: Line 10:
  
 
===constaxonomy===
 
===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 is smart enough to handle shared files that have been subsampled.
+
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)
 
  mothur > make.biom(shared=final.tx.1.subsample.1.pick.shared, constaxonomy=final.tx.1.cons.taxonomy)
Line 78: Line 78:
 
* 1.36.0 - Bug Fix: - repeat labels when combining mothur OTU labels with non mothur OTU labels, this can results in a duplicate "simple" label. This causes an incorrect taxonomy to be assigned to the OTU.
 
* 1.36.0 - Bug Fix: - repeat labels when combining mothur OTU labels with non mothur OTU labels, this can results in a duplicate "simple" label. This causes an incorrect taxonomy to be assigned to the OTU.
 
* 1.36.0 - remove paths from filenames to make compliant with qiime parser. - http://www.mothur.org/forum/viewtopic.php?f=3&t=3781&p=11241#p11241
 
* 1.36.0 - remove paths from filenames to make compliant with qiime parser. - http://www.mothur.org/forum/viewtopic.php?f=3&t=3781&p=11241#p11241
 +
* 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 14:44, 22 May 2019

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 (Note: mothur currently supports format version 1.0) 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"}}


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