I am working with pyrosequences of 16S. I tried to classify it using classify.seqs with the SILVA database provided by your site. The first time the output shown me that more than 60% of 12 independent libraries were Bacteroidetes, I founded this suspect. Today I run the same libraries again and now the output said that around 50% of the sequences are Acidobacteria :o I do not know why the classification are not consistent, Which could be the problem?
I use the default options
classify.seqs (fasta=S1_T_3.fasta, template=nogap.bacteria.fasta, taxonomy=silva.bacteria.silva.tax)
My fasta files are not aligned…
I am confuse about this, could you help me please?