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Get.sharedseqs

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The get.sharedotu command takes a list and group file and outputs a .names file for each distance. To run through the commands below use AbRecovery files.



Default settings

To execute the get.sharedotu() command you must provide a list and group file. By default this will output the otus shared by all the groups in your groupfile. For example:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups)

This will result in output to the screen looking like:

unique	0 - No otus shared by groups  A  B  C.
0.00	0 - No otus shared by groups  A  B  C.
0.01	1
0.02	2
0.03	3
0.04	3
0.05	4
0.06	5
0.07	6
...


The left column indicates the label for each line in the data set and the right column indicates the number of OTUs at this distance.

The .name output files look like: name|group|bin#

AY457715|C|59
AY457838|A|59
AY457774|B|59

Options

fasta

If you provide a fasta file mothur will also output a fasta file for each distance you specify:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, fasta=abrecovery.fasta)

The .fasta output files look like:

>AY457838|A|59
CCCTTAGAGTTTGATCCTGGCTCAGGACG...
>AY457774|B|59
CCCTTAGAGTTTGATCCTGGCTCAGGACG...
>AY457715|C|59
CCCTTAGAGTTTGATCCTGGCTCAGGACG...


label

There may only be a couple of lines in your list file that you are interested in. There are two options. You could: (i) manually delete the lines you aren't interested in from you list file; (ii) or use the label option.

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04-0.82)
0.04	3
0.82	1


Opening abrecovery.fn.0.04.names you would see the output as:

AY457701|C|45
AY457715|C|45
AY457838|A|45
AY457774|B|45
AY457747|C|45
AY457859|A|45
AY457695|C|46
AY457732|C|46
AY457860|A|46
AY457826|B|46
AY457767|B|46
AY457698|C|111
AY457855|A|111
AY457804|B|111

groups

The groups parameter allows you to see otus shared by specific groups or unique to a particular group. For example to see the otus at distance 0.04 unique to group A, you would enter the following:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, groups=A)
0.04	38

There are 38 otus unique to A at distance 0.04 and their names are listed in abrecovery.fn.0.04.names.


output

The output parameter allows you to have the .names file be in .accnos form so you can use it with the get.seqs, list.seqs and remove.seqs commands. For example:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, output=accnos)

Opening abrecovery.fn.0.04.names you would see the output as:

AY457701
AY457715
AY457838
AY457774
AY457747
AY457859
AY457695
AY457732
AY457860
AY457826
AY457767
AY457698
AY457855
AY457804