In analysing 16S rRNA sequences without mock community, how do we write command for get.groups?
With mock community it used to be
get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.fasta, groups=Mock)
In group I add = the list of samples, or you can make a accnos file with all the samples/groups inside. I am not sure what you are asking exactly, but in the mothur wiki is very well explained (at least was very useful for me)…
Thank you so much. The issue is that we did not sequence mock community in our study. Based on the advice offered by Pat that if we did not sequence mock community, then we don’t need to add it in the mothur analysis. The question is that in the get.group command where mock was placed what can we replace it with since we didn’t sequence mock.
Hi - if you don’t have a mock community then you can skip the get.groups/remove.groups steps where the mock community is extracted or removed.
Pat
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