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

Difference between revisions of "Split.groups"

From mothur
Jump to: navigation, search
(Revisions)
 
Line 1: Line 1:
The [[split.groups]] command reads a [[fasta file | fasta]] file or [[flow file | flow]] and [[group file | group]] file or [[Count_File | count]] and generates a fasta or flow file for each group in the groupfile.  To run this tutorial please download [[Media:Esophagus.zip | Esophagus dataset]].
+
The [[split.groups]] command reads a [[fasta file | fasta]] file or [[flow file | flow]] and [[group file | group]] file or [[Count_File | count]] or [[Fastq_File | fastq]] file and generates a fasta, flow or fastq files for each group in the groupfile.  To run this tutorial please download [[Media:Esophagus.zip | Esophagus dataset]].
 
 
  
Line 12: Line 12:
 
This command generates 3 files: esophagus.B.fasta, esophagus.C.fasta and esophagus.D.fasta
 
This command generates 3 files: esophagus.B.fasta, esophagus.C.fasta and esophagus.D.fasta
  
 +
or
 +
 +
mothur > split.groups(fastq=full.fastq, count=full.count_table)
  
 
==Options==
 
==Options==
Line 37: Line 40:
 
* 1.32.0 - Bug Fix: not splitting properly with a count file.
 
* 1.32.0 - Bug Fix: not splitting properly with a count file.
 
* 1.40.0 - Adds flow parameter.
 
* 1.40.0 - Adds flow parameter.
 +
* 1.42.0 - Adds fastq parameter. [https://github.com/mothur/mothur/issues/499  #499]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 16:31, 29 April 2019

The split.groups command reads a fasta file or flow and group file or count or fastq file and generates a fasta, flow or fastq files for each group in the groupfile. To run this tutorial please download Esophagus dataset.


Default Settings

mothur > split.groups(fasta=esophagus.fasta, group=esophagus.groups)

or

mothur > split.groups(flow=esophagus.flow, count=esophagus.count_table)

This command generates 3 files: esophagus.B.fasta, esophagus.C.fasta and esophagus.D.fasta

or

mothur > split.groups(fastq=full.fastq, count=full.count_table)

Options

name

The name parameter allows you add a names file with your fasta file and a name file will be generated for each group.

mothur > split.groups(fasta=esophagus.fasta, group=esophagus.groups, name=esophagus.names)

count

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. A count file will be created for each group.

mothur > split.groups(fasta=esophagus.fasta, count=esophagus.count_table)

groups

The groups parameter allows you to select groups to create files for. For example if you set groups=B-C, you will only get a esophagus.B.fasta, esophagus.B.names, esophagus.C.fasta, esophagus.C.names files.

mothur > split.groups(fasta=esophagus.fasta, group=esophagus.groups, name=esophagus.names, groups=B-C)

flow

The flow parameter is used to input your flow file.

Revisions

  • 1.28.0 - Added count parameter
  • 1.32.0 - Bug Fix: not splitting properly with a count file.
  • 1.40.0 - Adds flow parameter.
  • 1.42.0 - Adds fastq parameter. #499