When I’m looking at metagenomic 18S sequences from eukaryotes, what are the changes that I need to put in the 454 SOP? I’m guessing:

  1. use the eukaryotic Silva reference file instead of the bacterial one.
  2. use -something- instead of the RDP reference files.

Is this correct? If so, what can I use instead of the RDP files?
Many thanks!

Sorry, I meant the RDP training files.

You could try the silva.eukarya.fasta/nogap.eukarya.fasta and silva.eukarya.silva.tax or silva.eukarya.ncbi.tax files. This is a poorly developed area so you might prepare yourself to do some curation of these files.