classify.seq

Commands in mothur
1

Hi!
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.


Thanks!
2

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

3

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


Thanks!
4

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.

Pat