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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]], [[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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The [[list.seqs]] command will write out the names of the sequences found within a [[fastq file | fastq]], [[fasta file | fasta]], [[name file | name]], [[group file | group]], [[Count_File | count]], [[list file | list]], or [[align.report file | 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.
  
 
__NOTOC__
 
__NOTOC__
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==Options==
 
==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.
 
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.
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===fastq option===
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The fastq option is used as presented in the following command:
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mothur > list.seqs(fastq=test.fastq)
  
 
===fasta option===
 
===fasta option===
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  59_10_17
 
  59_10_17
 
  ...
 
  ...
 
  
 
===name option===
 
===name option===
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  mothur > list.seqs(name=esophagus.names)
 
  mothur > list.seqs(name=esophagus.names)
  
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===count option===
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The [[Count_File | 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.  It can also contain group information.
  
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mothur > list.seqs(count=esophagus.count_table)
  
 
===group option===
 
===group option===
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  mothur > list.seqs(group=esophagus.groups)
 
  mothur > list.seqs(group=esophagus.groups)
 
 
  
 
===alignreport option===
 
===alignreport option===
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  mothur > list.seqs(alignreport=esophagus.align.report)
 
  mothur > list.seqs(alignreport=esophagus.align.report)
 
  
 
===list option===
 
===list option===
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  mothur > list.seqs(list=esophagus.fn.list)
 
  mothur > list.seqs(list=esophagus.fn.list)
 
  
 
===taxonomy option===
 
===taxonomy option===
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==Revisions==
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* 1.28.0 Added count option
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* 1.33.0 Added fastq option
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* 1.40.0 - Allow for () characters in taxonomy definitions. [https://github.com/mothur/mothur/issues/350 #350]
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 14:56, 29 March 2018

The list.seqs command will write out the names of the sequences found within a fastq, fasta, name, group, count, 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.

fastq option

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

mothur > list.seqs(fastq=test.fastq)

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)

count option

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. It can also contain group information.

mothur > list.seqs(count=esophagus.count_table)

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)

taxonomy option

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

mothur > list.seqs(taxonomy=esophagus.silva.full.taxonomy)


Revisions

  • 1.28.0 Added count option
  • 1.33.0 Added fastq option
  • 1.40.0 - Allow for () characters in taxonomy definitions. #350