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

Difference between revisions of "Make.shared"

From mothur
Jump to: navigation, search
(Revisions)
(Inputting list data for multiple samples)
Line 12: Line 12:
 
  mothur > make.shared(list=98_sq_phylip_amazon.an.unique_list, count=amazon.count_table)
 
  mothur > make.shared(list=98_sq_phylip_amazon.an.unique_list, count=amazon.count_table)
  
This command will generate two types of files: a [[shared file]] (98_sq_phylip_amazon.an.shared) and rabund files for each group (98_sq_phylip_amazon.an.pasture.rabund and 98_sq_phylip_amazon.an.rainforest.rabund).  This parsing was not previously possible; one had to generate separate distance matrices for each group and run DOTUR on each matrix.  Because clustering can change when different sequences are included or excluded it was possible that sequences would wind up in OTUs different than those they were in when all of the data was considered together.
+
This command will generate a [[shared file]] (98_sq_phylip_amazon.an.shared).
  
You can also create a shared file from a biom file, http://biom-format.org/documentation/biom_format.html.
+
==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)
 
  mothur > make.shared(biom=example.biom)

Revision as of 16:40, 24 December 2015

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).

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.