I do not know if this is very amateur question but I want to know if I use classify.seq command on my raw fasta sequences and silva taxonomy, will I get the correct taxonomy information.
I have 500000 sequences and when I use this command all the 500000 sequences get taxonomy. I am wondering if it is correct method I am adopting.


I would probably use the RDP or greengenes references that we provide for running classify.seqs.

Thank you Dr. Schloss!
So, by this you mean that if all the sequences are getting some taxonomy, then it is correct.


Well, whether or not they are the correct classification is another kettle of fish. But if you get a classification and no error messages, then he command executed properly.