get.groups from shared file

Commands in mothur
1

Hi!

I have a .shared file that contains several groups. Now I want to extract the original fasta sequences (i.e. the raw sequences with primers and barcodes) from one of those groups.

I have tried the following:
get.groups(shared=final.shared, groups=control, group=test.groups, fasta=original.fasta)

I get a .fasta file with sequences from the group in question. However there are MORE sequences in this .fasta file than if I sum the OTU line of that sample in the final.shared file; 2944 vs. 2600. 2944 is the number of sequences of the “control” group in the test.groups file. So, I essentially get all raw sequences from the control group represented in my test.groups file, not those only represented in my .shared file.

What do I need to do to get only the sequences that are represented in the .shared file?

Kind regards, Anke.

2

You are correct the get.groups command relies on the group file to determine the split. It looks like there may be a file mismatch between your shared and group files. Here’s how you would get the results you are looking for:

mothur > list.seqs(list=theListFileYouUsedToCreateTheSharedFile) - list sequences you want
mothur > get.seqs(group=test.groups) - select sequences from list file you want to use
mothur > make.shared(list=current, group=current) - create shared file
mothur > get.groups(shared=current, groups=control, group=current, fasta=original.fasta) - select sequences from the control group