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Difference between revisions of "List.seqs"

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The [[list.seqs]] command will write out the names of the sequences found within a [[fasta file | fasta]], [[name file | name]], [[group file | group]], or [[align.report file]].  This could be useful for using the [[get.seqs]] and [[remove.seqs]] commands as well as to generate a [[group file]].    To complete this analysis, you need to download the folder compressed in the [[Media:Esophagus.zip | Esophagus.zip]] archive.
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The [[list.seqs]] command will write out the names of the sequences found within a [[fasta file | fasta]], [[name file | name]], [[group file | group]], [[list file | list]], or [[align.report file]].  This could be useful for using the [[get.seqs]] and [[remove.seqs]] commands as well as to generate a [[group file]].    To complete this analysis, you need to download the folder compressed in the [[Media:Esophagus.zip | Esophagus.zip]] archive.
  
 
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  59_10_17
 
  59_10_17
 
  ...
 
  ...
 
 
[[Category:Commands]]
 
 
  
  
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  mothur > list.seqs(alignreport=esophagus.align.report)
 
  mothur > list.seqs(alignreport=esophagus.align.report)
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===list option===
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The list option is used as presented in the following command:
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mothur > list.seqs(list=esophagus.fn.list)
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[[Category:Commands]]

Revision as of 20:23, 26 January 2010

The list.seqs command will write out the names of the sequences found within a fasta, name, group, list, or align.report file. This could be useful for using the get.seqs and remove.seqs commands as well as to generate a group file. To complete this analysis, you need to download the folder compressed in the Esophagus.zip archive.


Options

At least one of the following options must be used. Each of these options will generate a file ending in accnos that contains a single column containing the list of the sequences contained in the input file.

fasta option

The fasta option is used as presented in the following command:

mothur > list.seqs(fasta=esophagus.fasta)

The resulting esophagus.accnos file looks something like:

59_10_1
59_10_10
59_10_11
59_10_13
59_10_15
59_10_16
59_10_17
...


name option

The name option is used as presented in the following command (be sure to run unique.seqs on esophagus.fasta first):

mothur > list.seqs(name=esophagus.names)


group option

The group option is used as presented in the following command:

mothur > list.seqs(group=esophagus.groups)


alignreport option

The alignreport option is used as presented in the following command:

mothur > list.seqs(alignreport=esophagus.align.report)


list option

The list option is used as presented in the following command:

mothur > list.seqs(list=esophagus.fn.list)