Dear All,
I have a question confused me for a while that the OTU classification could be further into one specific genus, which means that a genus could be separated into several OTUs. I am wondering whether it is normal or not? The commands are:
mothur cluster.split(fasta=test.unique.filter.unique.precluster.fasta,count=test.unique.filter.unique.precluster.count_table,taxonomy=test.unique.filter.unique.precluster.seed_v123.wang.taxonomy,splitmethod=classify,taxlevel=6,large=T,processors=8)
mothur
classify.otu(list=test.unique.filter.unique.precluster.an.unique_list.list,count=test.unique.filter.unique.precluster.count_table,taxonomy=test.unique.filter.unique.precluster.seed_v123.wang.taxonomy,label=0.03,cutoff=80,threshold=90)
Just like following Otu0001 and Otu0003, both of which are belonged to Pseudomonas.
Otu0001 9367 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(94);Pseudomonas_unclassified(94);Pseudomonas_unclassified(94);
Otu0002 6477 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonadaceae_unclassified(91);Pseudomonadaceae_unclassified(91);Pseudomonadaceae_unclassified(91);
Otu0003 2626 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(80);Pseudomonas_unclassified(80);Pseudomonas_unclassified(80);
Thanks,
Rain