mothur

Output Lists of OTUs for Each Group in Separate Files

Hello,

I am currently looking through the commands and trying to figure out the best command to use to output a fasta or list for each group, that contains all of the OTU’s present within that group. Is the only way to do this to use get.otus for each group individually, or can this be achieved with some other command that I am missing?

Any advice is appreciated!

You can use the split.groups command, https://mothur.org/wiki/split.groups/.

mothur > split.groups(fasta=yourFastaFile, list=yourListFile, count=yourCountFile) - creates a *.fasta, *.list and *.count file for each group

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