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Difference between revisions of "Rename.seqs"

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  mothur > rename.seqs(fasta=final.fasta, count=final.count_table)
 
  mothur > rename.seqs(fasta=final.fasta, count=final.count_table)
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===file===
 +
The file option allows you to provide a 2 or 3 column file. The first column contains the file type: fasta or qfile. The second column is the filename, and the optional third column can be a group name. If there is a third column, all sequences in the file will be assigned to that group.  This can be helpful when renaming data separated into samples.
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===map===
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The map parameter allows you to enter a map file.  The map file is generated by the rename.seqs command and maps the new name to the old name.  Providing a map file allows you to "undo" a previous rename.seqs command.  This can be helpful if you want to run an analysis with simplified names to save space and then replace the original names at any point in the analysis.
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===qfile===
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The qfile allows you to provide an associated quality file.
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=== contigsreport===
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The contigsreport allows you to provide an associated contigsreport file.
  
 
===delim===
 
===delim===
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* 1.32.0 - First Introduced.
 
* 1.32.0 - First Introduced.
 
* 1.36.0 - Adds count, delim, and placement parameters
 
* 1.36.0 - Adds count, delim, and placement parameters
 +
* 1.37.0  - Adds file, map, qfile and contigsreport parameters. [https://github.com/mothur/mothur/issues/132 #132]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 20:30, 11 April 2016

Provided with a fasta-formatted sequence file and group file, the rename.seqs rename the sequences appending the group name to the sequence name.

Default

The rename.seqs command requires and fasta and group file.

mothur > rename.seqs(fasta=final.fasta, group=final.groups)

This command will create final.renamed.fasta and final.renamed.groups files. The sequence names will look like: GQY1XT001C296C_F003D000. GQY1XT001C296C was the original sequence name and F003D000 is the sample it came from.

Options

name

If your dataset uses a name file, you will want to include it to avoid downstream name mismatch issues.

mothur > rename.seqs(fasta=final.fasta, group=final.groups, name=final.names)

count

The count parameter allows you to provide a count file.

mothur > rename.seqs(fasta=final.fasta, count=final.count_table)

file

The file option allows you to provide a 2 or 3 column file. The first column contains the file type: fasta or qfile. The second column is the filename, and the optional third column can be a group name. If there is a third column, all sequences in the file will be assigned to that group. This can be helpful when renaming data separated into samples.

map

The map parameter allows you to enter a map file. The map file is generated by the rename.seqs command and maps the new name to the old name. Providing a map file allows you to "undo" a previous rename.seqs command. This can be helpful if you want to run an analysis with simplified names to save space and then replace the original names at any point in the analysis.

qfile

The qfile allows you to provide an associated quality file.

contigsreport

The contigsreport allows you to provide an associated contigsreport file.

delim

The delim parameter allow you to enter the character or characters you would like to separate the sequence name from the group name. Default='_'.

mothur > rename.seqs(fasta=final.fasta, group=final.groups, delim=::)

The resulting names would look like: GQY1XT001A006L::F003D144.

placement

The placement parameter allows you to indicate whether you would like the group name appended to the front or back of the sequence name. Options are front or back. Default=back.

mothur > rename.seqs(fasta=final.fasta, group=final.groups, placement=front)

The resulting names would look like: F003D000_GQY1XT001C296C.

Revisions

  • 1.32.0 - First Introduced.
  • 1.36.0 - Adds count, delim, and placement parameters
  • 1.37.0 - Adds file, map, qfile and contigsreport parameters. #132