I used the get.groups command with the list option. My problem is that I do not get a single new list file, but 9. I was not able to find out what the difference between the files is and which to use. They are a pain to look at and find out, even with a lister or the “head”-command. i need a single list file to make.shared . Do you know what to do?
THanks,
Fabian
mothur > get.groups(list=stability2.trim.contigs.good.unique.good.filter.unique.precluster.pick.silva.wang.pick.tx.list, group=stability2.contigs.good.groups, groups=a bunch of ~30 groups I do not want to tell)
Selected 3895083 sequences from your group file.
Selected 19888 sequences from your list file.
mothur > get.groups(list=stability2.trim.contigs.good.unique.good.filter.unique.precluster.pick.silva.wang.pick.tx.list, group=stability2.contigs.good.groups, groups=a bunch of ~30 groups I do not want to tell)
mothur > list.seqs(group=current) - list sequences in the groups you selected
mothur > get.seqs(list=stability2.trim.contigs.good.unique.good.filter.unique.precluster.pick.silva.wang.pick.tx.list, accnos=current) - select the sequences from the list file that are in the groups you want.
I think I figured it out. I used the wrong list file.
The file that was shown as the latest (current) list file was not the proper one to use. stability2.trim.contigs.good.unique.good.filter.unique.precluster.pick.silva.wang.pick.tx.list came from the “phylotype” command and does not seem to be fully compatible with the list option of the get.groups command. I should have used stability2.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list which came out of the OTU clustering. Here I get a list file for each label. I still kind of think I should get a single list file as output because the input is a single list file that I pick sequences from, but now I understand what I have there and can work with it.
Best,
Fabian
mothur > get.groups(list=stability2.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list, group=stability2.contigs.good.groups, groups= a bunch of ~30 groups)
Selected 3895083 sequences from your group file.
Selected 19888 sequences from your list file.