We will be offering an R workshop December 18-20, 2019. Learn more.

Difference between revisions of "Make.shared"

From mothur
Jump to: navigation, search
(Revisions)
 
(One intermediate revision by the same user not shown)
Line 43: Line 43:
 
* 1.39.0 Eliminates zero abundance OTUs created by some floating point biom files converted to shared files.
 
* 1.39.0 Eliminates zero abundance OTUs created by some floating point biom files converted to shared files.
 
* 1.41.0 Adds count file to shared file option in make.shared command. [https://github.com/mothur/mothur/issues/519  #519]  
 
* 1.41.0 Adds count file to shared file option in make.shared command. [https://github.com/mothur/mothur/issues/519  #519]  
 +
* 1.42.0 Expands make.shared to allow for count files with no groups. [https://github.com/mothur/mothur/issues/563  #563]
 +
* 1.42.0 Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. [https://github.com/mothur/mothur/issues/583  #583]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 17:00, 29 April 2019

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)

or you can convert a count file to a shared file.

mothur > make.shared(count=amazon.count_table, label=0.03)

This command will generate a shared file.

Creating a shared file from a biom file

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)

Options

label

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)

groups

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)

Revisions

  • 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.
  • 1.41.0 Adds count file to shared file option in make.shared command. #519
  • 1.42.0 Expands make.shared to allow for count files with no groups. #563
  • 1.42.0 Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. #583