Beginner questions: Working step for organism identification

Hello everyone, I am the beginner for this area of study, and I have no one to ask these simple questions.

I want to identify organism using NGS sequencing. I read from tutorial and I known that I have to make contigs and filter unusual sequences out. Then, compare filtered sequence with database (classify command).

But, There are some unclear topics forme.

  1. Is it true for my work flow? any suggestions? What are the steps that I should do? Does pre.cluster need for my work?
  2. Can I use other databases in Mothur?
  3. If I can use other databases, where can I find .tax file? How to determine taxon in classify command if I use other databases?
  4. I already tried to align with downloaded database (not SILVA), but the muthur system told me that sequences not align. I aligned them in BioEdit and saved into .fasta, but, when I tried to align again, system cannot open that file. How to solve it?

Thank you very much.

Welcome! I’d encourage you to go through the MiSeq SOP. You’ll find answers to most of your questions there. Once you’ve done that come back with any more specific questions you might have.