Problem with get.sharedseqs

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.


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


get.sharedseqs(,sharedgroups=G1-G16-G17-G20-G29-G30-G32-G4-G18-G19-G21-G25-G28-G31) 0.05 9

Output File Names:

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