Hi, i am trying to run get.sharedseqs to get the name of OTUs that shared sequences between groups G1, G5 and G10, but when i do groups=G1-G5-G10, i get shared sequences for all the groups that are alphabetically in between i.e. G1 to G5 and G5 to G10!!! I tried commas but it didn’t work. Please help.
O.A.
Could you post the whole command you are running? The get.sharedseqs command does not have a groups option. It has a group parameter used to input the group file. The uniquegroups parameter allows you to see sequences belonging to OTUs unique to specific groups or unique to a particular group. The sharedgroups parameter allows you to see sequences belonging to OTUs that contain specific groups or a particular group.
Thanks Sarah, correct. I mean “sharedgroups”. Here is my code and my output. The output here include for example all the groups between G1 and G16 i.e. G11, G12, …which is not in the code.
many thanks
OA
get.sharedseqs(shared=final.pick.an.shared,sharedgroups=G1-G16-G17-G20-G29-G30-G32-G4-G18-G19-G21-G25-G28-G31)
0.05 9
Output File Names:
final.pick.an.0.05.selected_groups.shared.seqs
Otu00001|G12|22
Otu00001|G15|256
Otu00001|G16|4
Otu00001|G17|48
Otu00001|G18|12
Otu00001|G19|18
Otu00001|G1|23
Otu00001|G20|55
Otu00001|G21|181
Otu00001|G22|618
Otu00001|G23|6789
Otu00001|G24|1116
Otu00001|G25|14
Otu00001|G26|301
Otu00001|G27|773
Otu00001|G28|12
Otu00001|G29|20
Otu00001|G30|41
Otu00001|G31|4
Otu00001|G32|1
Otu00001|G4|1
Otu00001|G5|16
Otu00001|G9|25
Otu00007|G10|8
Otu00007|G11|12
Otu00007|G12|101
Otu00007|G13|14
Otu00007|G14|11
Otu00007|G15|1
Otu00007|G16|10
Otu00007|G17|177
Otu00007|G18|86
Otu00007|G19|250
Otu00007|G1|211
Otu00007|G20|222
Otu00007|G21|310
Otu00007|G22|161
Otu00007|G23|69
Otu00007|G24|26
Otu00007|G25|25
Otu00007|G26|30
Otu00007|G27|141
Otu00007|G28|21
Otu00007|G29|19
Otu00007|G30|158
Otu00007|G31|43
Otu00007|G32|16
Otu00007|G4|1
Otu00007|G5|51
Otu00007|G8|15
Otu00007|G9|20
Otu00012|G11|7
Otu00012|G12|80
Otu00012|G13|13
Otu00012|G14|8
Otu00012|G15|33
Otu00012|G16|6
Otu00012|G17|112
Otu00012|G18|78
Otu00012|G19|10
Otu00012|G1|190
Otu00012|G20|44
Otu00012|G21|104
Otu00012|G22|25
Otu00012|G23|17
Otu00012|G24|20
Otu00012|G25|38
Otu00012|G26|6
Otu00012|G27|45
Otu00012|G28|139
Otu00012|G29|156
Otu00012|G30|367
Otu00012|G31|7
Otu00012|G32|18
Otu00012|G4|2
Otu00012|G5|14
Otu00012|G8|12
Otu00012|G9|9
Otu00014|G11|1
Otu00014|G12|47
Otu00014|G14|2
Otu00014|G15|387
Otu00014|G16|2
Otu00014|G17|15
Otu00014|G18|16
Otu00014|G19|22
Otu00014|G1|117
Otu00014|G20|84
Otu00014|G21|88
Otu00014|G22|28
Otu00014|G23|204
Otu00014|G24|70
Otu00014|G25|30
Otu00014|G26|15
Otu00014|G27|44
Otu00014|G28|91
Otu00014|G29|65
Otu00014|G30|10
Otu00014|G31|17
Otu00014|G32|2
Otu00014|G4|11
Otu00014|G9|97
Otu00019|G12|1
Otu00019|G13|1
Otu00019|G14|2
Otu00019|G15|1
Otu00019|G16|29
Otu00019|G17|253
Otu00019|G18|60
Otu00019|G19|46
Otu00019|G1|29
Otu00019|G20|27
Otu00019|G21|218
Otu00019|G22|12
Otu00019|G23|12
Otu00019|G24|7
Otu00019|G25|69
Otu00019|G26|7
Otu00019|G28|17
Otu00019|G29|19
Otu00019|G30|247
Otu00019|G31|25
Otu00019|G32|90
Otu00019|G4|1
Otu00019|G5|2
Otu00019|G9|18
Otu00021|G11|2
Otu00021|G12|13
Otu00021|G15|11
Otu00021|G16|2
Otu00021|G17|155
Otu00021|G18|30
Otu00021|G19|20
Otu00021|G1|53
Otu00021|G20|41
Otu00021|G21|115
Otu00021|G22|58
Otu00021|G23|12
Otu00021|G24|13
Otu00021|G25|103
Otu00021|G26|1
Otu00021|G27|22
Otu00021|G28|106
Otu00021|G29|113
Otu00021|G30|124
Otu00021|G31|49
Otu00021|G32|54
Otu00021|G4|1
Otu00021|G5|4
Otu00021|G8|1
Otu00021|G9|1
Otu00025|G12|44
Otu00025|G13|6
Otu00025|G14|1
Otu00025|G15|17
Otu00025|G16|10
Otu00025|G17|35
Otu00025|G18|43
Otu00025|G19|20
Otu00025|G1|103
Otu00025|G20|17
Otu00025|G21|39
Otu00025|G22|53
Otu00025|G23|52
Otu00025|G24|65
Otu00025|G25|99
Otu00025|G26|10
Otu00025|G27|47
Otu00025|G28|84
Otu00025|G29|103
Otu00025|G30|37
Otu00025|G31|30
Otu00025|G32|65
Otu00025|G4|2
Otu00025|G5|15
Otu00025|G8|3
Otu00025|G9|2
Otu00067|G10|27
Otu00067|G12|12
Otu00067|G13|1
Otu00067|G14|6
Otu00067|G15|20
Otu00067|G16|4
Otu00067|G17|15
Otu00067|G18|13
Otu00067|G19|23
Otu00067|G1|6
Otu00067|G20|5
Otu00067|G21|34
Otu00067|G22|17
Otu00067|G23|9
Otu00067|G24|22
Otu00067|G25|20
Otu00067|G26|1
Otu00067|G27|23
Otu00067|G28|15
Otu00067|G29|21
Otu00067|G30|22
Otu00067|G31|1
Otu00067|G32|14
Otu00067|G4|1
Otu00067|G5|9
Otu00067|G8|1
Otu00067|G9|6
Otu00146|G16|6
Otu00146|G17|27
Otu00146|G18|3
Otu00146|G19|2
Otu00146|G1|7
Otu00146|G20|6
Otu00146|G21|12
Otu00146|G23|2
Otu00146|G24|1
Otu00146|G25|16
Otu00146|G27|7
Otu00146|G28|3
Otu00146|G29|15
Otu00146|G30|12
Otu00146|G31|11
Otu00146|G32|23
Otu00146|G4|2
Correct, these OTUs contain sequences from the all of the groups you listed but may contain sequences from other groups. If you want OTUs that contain ONLY sequences from the groups you listed, then you want to use the uniquegroups parameter.
sharedgroups= includes all your groups and anyone else
uniquegroups= includes all your groups and no one else