Hey everyone, I have a problem creating the group file - the problem is that Im not really sure which type of file to make. I have been following the esophageal community analysis pipeline. I have a fasta file with all my sequences that comes from 14 different samples. Together with a database file I created and alignment, screened it, filtered it and used the dist.seq.I then clustered the files to make OTUs. Now I need to do the make.shared command but don’t know how to make the groups file that is needed. Any help is very much appreciated - Im a complete beginner!
Elisabeth
Welcome to the mothur community! Pat has written 2 example analysis’s you may find helpful as well: http://www.mothur.org/wiki/454_SOP and http://www.mothur.org/wiki/MiSeq_SOP. Group files are created in two ways. If you have barcodes and primers you can create an oligos file, http://www.mothur.org/wiki/Oligos_File, and when you include an oligos file with commands like trim.seqs mothur will create a group file for you. Mothur also has a command called make.group, http://www.mothur.org/wiki/Make.group. This command can be used if you have a fasta file or several fasta files you want to assign group values to. It sounds like this is the command you will want.
-Sarah