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The make.shared command reads a list and group file or biom file and creates a .shared file as well as a rabund file for each group.
Inputting list data for multiple samples
The Amazonian data set actually represents sequences from two samples - one from soil collected at a pasture site and a rainforest site. Looking at the file amazon.groups you can see which sequences belong to the pasture and rainforest sites. There is no limit to the number of groups you can have.
mothur > make.shared(list=98_sq_phylip_amazon.an.list, group=amazon.groups)
or if you used a count file instead of a name file and group file:
mothur > make.table(name=amazon.names, group=amazon.groups) mothur > cluster(phylip=98_sq_phylip_amazon.dist, count=amazon.count_table) mothur > make.shared(list=98_sq_phylip_amazon.an.unique_list, count=amazon.count_table)
This command will generate a shared file (98_sq_phylip_amazon.an.shared).
You can also convert a biom file, http://biom-format.org/documentation/biom_format.html. (Note: mothur currently supports format version 1.0) to a shared file to import your data into mothur.
mothur > make.shared(biom=example.biom)
There may only be a couple of lines in your OTU data that you are interested in summarizing. There are two options. You could: (i) manually delete the lines you aren't interested in from you rabund, sabund, list, or shared file; (ii) or use the label option. If you only want to read in the data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
mothur > make.shared(list=98_sq_phylip_amazon.fn.list, group=amazon.groups, label=unique-0.03-0.05-0.10)
You can use the groups parameter to specify which groups you want included in your analysis:
mothur > make.shared(list=98_sq_phylip_amazon.fn.list, group=amazon.groups, groups=forest-pasture)
- 1.22.0 Removed ordergroup parameter.
- 1.25.0 added biom parameter
- 1.28.0 added count parameter
- 1.36.0 mothur no longer checks for biom matrix type to allow for more flexibility.
- 1.36.0 rabund files are no longer outputted. Mothur will create a rabund file with the get.rabund command.
- 1.39.0 Eliminates zero abundance OTUs created by some floating point biom files converted to shared files.