classify.otu and then organize by sample?


I am using the classify.seqs and classify.otu commands to get a consensus taxonomy for my OTUs. However, the confusing thing is that the consensus taxonomy I get out at the 0.03 distance level is not related at all to my samples. Here are the first 5 lines out of classify.otu:

OTU Size Taxonomy
1 846 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Alteromonadales(100);Psychromonadaceae(100);Psychromonas(100);
2 741 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Alteromonadales(100);Psychromonadaceae(100);Psychromonas(100);
3 375 Bacteria(100);Proteobacteria(100);Epsilonproteobacteria(100);Campylobacterales(100);Helicobacteraceae(100);Sulfurovum(100);
4 380 Bacteria(100);Proteobacteria(100);Epsilonproteobacteria(100);Campylobacterales(100);Helicobacteraceae(100);Sulfurovum(100);
5 490 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Alteromonadales(100);Psychromonadaceae(100);Psychromonas(100);

However, I don’t know if OTU 1 is present in sample 1 or sample 2 or in both. The taxonomy that comes out of the classify.seqs command is more useful because it is organized by sample. As in below:

taxlevel rankID taxon daughterlevels total KM1A KM3N KM2I 41_3a 39_2a 45_3a
0 0 Root 1 0 0 0 0 0 0 0
1 0.1 Bacteria 10 28787 2366 1407 4250 10145 7508 3111

Is there a way to get a consensus taxonomy for my OTUs and to see which of the OTUs would be assigned to each sample? Getting the consensus taxonomy for each OTU sounds good in theory but if I cannot see how those OTUs are distributed across my samples then it doesn’t seem very useful. I think this should be possible, unless I have misunderstood how the classify.otu command works.

Thank you,

Have you generated a shared file using read.otu(list=???.list, group=???.groups)? Here the columns will indicate the number of times each OTU/phylotype was seen in each group. The ordering of these columns corresponds to the ordering in the consensus file.