classify.otu

Commands in mothur
1

Hi,

I would like to make the claim that a certain bacterial family is especially diverse/species rich. Therefore I ran the classify OTU command for OTUs at the 3% level

classify.otu(taxonomy=joint.unique.precluster.pick.filter.good.good.pick.silva.taxonomy,list=joint.unique.precluster.pick.filter.good.good.pick.an.list,name=joint.unique.precluster.pick.good.good.pick.names,group=joint.pick.good.good.pick.groups,label=0.03)

For ~family level I extract all lines where taxlevel=5 from the tax.summary file. Does the column ‘total’ in the tax.summary file give me the total number of OTUs in the respective taxon (family) across all my samples?

taxlevel rankID taxon daughterlevels total
5 0.1.4.2.1.2 Flavobacteriaceae 6 35

Does that mean there is a total of 35 3% OTUs that are Flavobacteriaceae across all samples?
Does all this make sense to you?
Thanks!

2

I am asking because the ‘total’ column in the tax.summary file that is the output of the classify.otu command does not reflect the row sum across the different samples, but gives a lower number. This is unlike a tax.summary on sequences where the counts add up to the total. Is that because some of the OTUs found across samples are identical and therefore they are not summed up to the total?