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While the bin.seqs command reports the OTU number for all sequences, the get.oturep command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. A .rep.fasta and .rep.names file or .rep.count_table file is generated for each OTU definition. For this tutorial, download and decompress AmazonData.zip.
To run the get.oturep command you must provide either a phylip-formatted distance matrix or a column-formatted distance matrix, together with a list file whose sequence names are complementary to the names in the distance matrix. (An exception is that a distance file is not required if you specify method=abundance.) For example,
mothur > get.oturep(phylip=98_sq_phylip_amazon.dist, list=98_sq_phylip_amazon.an.list)
mothur > get.oturep(column=98_lt_column_amazon.dist, name=amazon.names, list=98_sq_phylip_amazon.an.list)
The .rep.names file will look like:
U68589 U68589 U68590 U68590 U68591 U68591 U68687 U68687,U68592 U68654 U68649,U68639,U68606,U68654,U68593 U68594 U68594 U68636 U68636,U68631,U68666,U68595 U68614 U68629,U68617,U68614,U68596 ...
or with a count file:
mothur > get.oturep(phylip=98_sq_phylip_amazon.dist, list=98_sq_phylip_amazon.an.unique_list, count=amazon.count_table)
mothur > get.oturep(column=98_lt_column_amazon.dist, list=98_sq_phylip_amazon.an.unique_list, count=amazon.count_table)
The .rep.count_table file will look like:
... U68589 1 U68590 1 U68591 1 U68687 2 U68654 5 U68594 1 U68636 4 U68614 4 ...
The representative sequences are named identically to the names given in the input file with the addition of the OTU number and number of sequences represented separated by a tabs as follows:
>name OTU#|sequences represented sequence....
The cutoff parameter allows you to limit the distances read into memory.
If you provide a fasta file, mothur will generate 12 fasta-formatted files (one per OTU definition in the list file) that each contain the same number of sequences as there are OTUs for that OTU definition. If there are three or more sequences in an OTU, the representative sequence is that sequence which is the minimum distance to the other sequences in the OTU. For example, the file 98_sq_phylip_amazon.fn.0.10.fasta contains the following output:
mothur > get.oturep(phylip=98_sq_phylip_amazon.dist, list=98_sq_phylip_amazon.an.list, fasta=amazon.fasta)
>U68589 1|1 TAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACA... >U68590 2|1 TAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCA... >U68591 3|1 CGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGA... >U68687 4|2 TAATACAGAGGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGAGGTAAG... >U68654 5|5 TAATACGGNCGGGGCAANCGTTGTTCGGAATTACTGGGCGTAAAGGGCTCGTAGGCGGCCAACTAAG... >U68594 6|1 TAATCCCAAGGGTGCAANCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTTGTTAAG... ...
A names file indicating sequence names that are identical to a references sequence, may be inputted into the get.oturep() command so that the fasta and list files are complementary. The following command illustrate this:
mothur > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.unique.fasta, list=98_sq_phylip_amazon.fn.list)
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.
mothur > get.oturep(column=96_lt_column_amazon.dist, count=amazon.count_table, fasta=amazon.unique.fasta, list=98_sq_phylip_amazon.fn.unique_list)
There may only be a couple of lines in your OTU data that you are interested in running through get.oturep(). There are two options. You could: (i) manually delete the lines you aren't interested in from your list 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 > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.fasta, list=98_sq_phylip_amazon.fn.list, label=unique-0.03-0.05-0.10)
You may want to sort the output you get from the get.oturep command. The sorted option allows you to indicate how you want the output sorted. You can sort by sequence name, bin number, bin size or group. The default is no sorting, but your options are name, bin, size, or group.
mothur > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.fasta, list=98_sq_phylip_amazon.fn.list, label=unique-0.03-0.05-0.10, sorted=name)
The large parameter allows you to indicate that your distance matrix is too large to fit in RAM. The default value is false.
mothur > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.fasta, list=98_sq_phylip_amazon.fn.list, label=unique-0.03-0.05-0.10, large=true)
The group parameter allows you to provide a group file.
mothur > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.fasta, list=98_sq_phylip_amazon.fn.list, group=amazon.groups)
The groups parameter allows you to indicate that you want representative sequences for each group specified for each OTU, group name should be separated by dashes. ex. groups=A-B-C.
mothur > get.oturep(column=96_lt_column_amazon.dist, name=amazon.names, fasta=amazon.fasta, list=98_sq_phylip_amazon.fn.list, group=amazon.groups, groups=forest-pasture)
The weighted parameter allows you to indicate that want to find the weighted representative. You must provide a name file to set weighted to true. The default value is false. The representative is found by selecting the sequence that has the smallest total distance to all other sequences in the OTU. If a tie occurs the smallest average distance is used. For weighted = false, mothur assumes the distance file contains only unique sequences, the list file may contain all sequences, but only the uniques are considered to become the representative. If your distance file contains all the sequences it would become weighted=true. For weighted=true, mothur assumes the distance file contains only unique sequences, the list file must contain all sequences, all sequences are considered to become the representative, but unique name will be used in the output for consistency.
The method parameter allows you to select the representative sequence based on either distance or abundance. The distance method finds the sequence with the smallest maximum distance to the other sequences. If tie occurs the sequence with smallest average distance is selected. The abundance method chooses the most abundant sequence in the OTU as the representative. It is not necessary to specify a distance file if the abundance method is used.
- 1.23.0 fasta parameter is no longer required.
- 1.28.0 Added count option
- 1.31.0 - added method parameter. http://www.mothur.org/forum/viewtopic.php?f=5&t=2131
- 1.33.0 - changed otu numbers to be labels
- 1.41.0 - Updates get.oturep command to use optiMatrix. Reduces time and memory needed. #465