Using different reference for each align.seqs and classify.seqs


I have a basic question. I got 16S MiSeq paired microbiome dataset and I did taxonomy annotation using mothur MiSeq SOP. In my annotation process, I used silva.v4.fasta as reference in align.seqs() step and for classify.seqs() step I used trainset18_062020.rdp.fasta as reference. Did I make mistake doing like this?

Thank you

For my research, I use the silva for the align step, but for classify I use silva, PR2 or whatever is better suited for the group I am studying (protists/prokaryotes/metazoans/etc).

So, all good, IMO


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