get.sharedseqs
The get.sharedseqs command takes a list and count file or shared file and outputs a *.shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify. To run through the commands below use Example files.
Default settings
To execute the get.sharedseqs command you must provide a list and count file or shared file. By default this will output the sequences found in the OTUs shared by all the groups in your count file or shared file. For example:
mothur > get.sharedseqs(list=final.opti_mcc.list, count=final.count_table)
or
mothur > make.shared(list=final.opti_mcc.list, count=final.count_table)
mothur > get.sharedseqs(shared=final.opti_mcc.shared)
This will result in output to the screen looking like:
0.03 55
The left column indicates the label for each line in the data set and the right column indicates the number of OTUs shared by all groups at this distance.
The .shared.seqs output files look like:
Otu001|F3D0|499
Otu001|F3D141|388
Otu001|F3D142|244
Otu001|F3D143|189
Otu001|F3D144|346
Otu001|F3D145|566
Otu001|F3D146|270
Otu001|F3D147|1316
Otu001|F3D148|750
Otu001|F3D149|770
Otu001|F3D150|265
Otu001|F3D1|351
Otu001|F3D2|3076
Otu001|F3D3|831
Otu001|F3D5|278
Otu001|F3D6|902
Otu001|F3D7|576
Otu001|F3D8|236
Otu001|F3D9|435
Otu002|F3D0|306
Otu002|F3D141|335
Otu002|F3D142|258
Otu002|F3D143|152
...
Options
fasta
If you provide a fasta file mothur will also output a fasta file for each distance you specify:
mothur > get.sharedseqs(list=final.opti_mcc.list, count=final.count_table, fasta=final.fasta)
The .shared.fasta output files look like:
>M00967_43_000000000-A3JHG_1_2107_20457_11366|F3D7|Otu010
TAC--GG-AG-GAT--GCA-A-G-C-G-T-T--GT-C-CGG-AT--TT-A-T-T--GG-GC--GT-A-AA-GC-GA-GT-G-CA-...
>M00967_43_000000000-A3JHG_1_1105_11964_4686|F3D0|Otu012
TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-CA-...
...
uniquegroups & sharedgroups
The uniquegroups parameter allows you to see sequences belonging to OTUs unique to specific groups or unique to a particular group. For example to see the sequences from OTUs unique to group F3D0 at distance 0.03, you would enter the following:
mothur > get.sharedseqs(list=final.opti_mcc.list, count=final.count_table, uniquegroups=F3D0)
0.03 14
There are 14 OTUs that are unique to F3D0 at distance 0.03 and their sequence names are listed in final.opti_mcc.0.03.unique.F3D0.shared.seqs.
Similarly, if you wanted the sequences from OTUs unique to groups F3D0 and F3D1 at distance 0.03, you would enter the following
mothur > get.sharedseqs(list=final.opti_mcc.list, count=final.count_table, uniquegroups=F3D0-F3D1, label=0.03)
0.03 1
There is 1 OTU that only contain sequences from groups F3D0 and F3D1 at a distance of 0.03. The file final.opti_mcc.0.03.unique.F3D0_F3D1.shared.seqs contains:
M00967_43_000000000-A3JHG_1_2110_20054_3531|F3D0|Otu301
M00967_43_000000000-A3JHG_1_1114_9368_6991|F3D1|Otu301
...
The sharedgroups parameter allows you to see sequences belonging to OTUs that contain specific groups or a particular group. For example to see the sequences from OTUs that contain sequences from group F3D0 at distance 0.03, you would enter the following:
mothur > get.sharedseqs(list=final.opti_mcc.list, count=final.count_table, sharedgroups=F3D0)
0.03 192
There are 192 OTUs that contain sequences from group F3D0 at distance 0.03 and their names are listed in final.opti_mcc.0.03.F3D0.shared.seqs.
Similarly, if you wanted the sequences from OTUs that contain sequences from F3D0 and F3D1 at a distance of 0.03, you would enter the following
mothur > get.sharedseqs(list=final.opti_mcc.list, count=final.count_table, sharedgroups=F3D0-F3D1)
0.04 125
There are 125 OTUs that are shared between F3D0 and F3D1 at a distance of 0.03. The file final.opti_mcc.0.03.F3D0_F3D1.shared.seqs contains:
M00967_43_000000000-A3JHG_1_1101_20262_22075|F3D6|Otu001
M00967_43_000000000-A3JHG_1_1114_13556_18457|F3D144|Otu001
M00967_43_000000000-A3JHG_1_1102_18640_14309|F3D3|Otu001
M00967_43_000000000-A3JHG_1_1108_5894_23389|F3D143|Otu001
M00967_43_000000000-A3JHG_1_2101_4780_15092|F3D2|Otu001
...
label
There may only be a couple of lines in your list file that you are interested in. You could either manually delete the lines you aren’t interested in from you list file or use the label option.
output
The output parameter allows you to have the .seqs file be in .accnos form so you can use it with the get.seqs, list.seqs and remove.seqs commands. For example:
mothur > get.sharedseqs(list=final.opti_mcc.list, count=final.count_table, output=accnos)
0.03 55
Opening final.opti_mcc.0.03.unique.selected_groups.accnos you would see the output as:
M00967_43_000000000-A3JHG_1_1101_20262_22075
M00967_43_000000000-A3JHG_1_1114_13556_18457
M00967_43_000000000-A3JHG_1_1102_18640_14309
M00967_43_000000000-A3JHG_1_1108_5894_23389
M00967_43_000000000-A3JHG_1_2101_4780_15092
...
Why do the venn diagram results vary from get.sharedseqs results?
Confusion can occur when you have a shared file with more groups than just the subset you are looking at in your venn diagram. For this example let’s look at a simple shared file like:
Full shared file:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 A 5 43 38 2 0 1
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
mothur > venn(groups=B-C)
Venn shared file with groups B and C selected:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
C = 0 unique OTUs
B = 2 unique OTUs
BC = 3 shared OTUs
mothur > get.sharedseqs(uniquegroups=B)
Get.sharedseqs with uniquegroups=B shared file:
label group numOtus Otu001 Otu002 Otu003 Otu004 Otu005
0.26 A 5 43 38 2 0 1
0.26 B 5 46 14 10 13 1
0.26 C 5 16 29 29 0 0
B = 1 unique OTUs
The difference between the two commands is the groups mothur is considering when finding the unique and shared OTUs. With the venn command, mothur only uses the groups provided by the groups parameter or if none are provided the first 4 groups in the file. This is done because there are limits to the drawing of the venn diagram. With more than 4 groups the picture becomes too complicated to be of use. In this example group A is not included which changes the shared and unique composition.The get.sharedseqs command does not have the limitations of the picture. You can set parameters with the sharedgroups and uniquegroups. The sharedgroups parameter means the OTUs MUST include the groups you listed, but MAY also include other groups. The uniquegroups parameter means the OTUs MUST include the groups you listed and ONLY the groups you listed.
For example:
mothur > get.sharedseqs(uniquegroups=B-C)
B-C = 0 unique OTUs (no Otus contains just sequences from B and C)
mothur > get.sharedseqs(sharedgroups=B-C)
B-C = 3 shared OTUs (3 Otus contains sequences from B and C and sequences from other groups)
Revisions
- 1.30.0 - added shared file option and changed unique and shared parameter names to uniquegroups and sharedgroups.
- 1.37.0 - Adds count parameter #133
- 1.40.0 - Speed and memory improvements for shared files. #357 , #347
- 1.46.0 - Fixes bug with get.sharedseqs shared file option
- 1.47.0 - Fixes bug with get.sharedseqs if no groups are provided.