After running through the MiSeq SOP I wanted to pull out the sequences for specific OTUs. I did this with get.seqs and used a list of the original names of the sequences by going into stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list and taking the unique names for my OTUs. I was able to generate a fasta file with the sequences however, when I run the sequences through NCBI nblast using 16s ribosomal sequences as my database several of the classifications are completely different from how mothur classified my OTUs. I’m not sure which is correct or if I’m doing something wrong. I’ve tried with greengenes and silva/rdp in the pipeline, but still had the same issue of miss classifying the sequences. Any help is appreciated.