Miseq 18S RDP equivalent files

Commands in mothur
1

Hello,

I’m trying to adapt the Miseq SOP to run 18S sequences from eukaryotes. I’ve run 16S a few times but I still consider myself a novice, especially when it comes to 18S.

My first thing to do was to replace the silva reference files with the eukaryotic versions (Silva.eukarya.fasta and silva.eukarya.silva.tax) as well as tweaking pcr.seqs and screen.seqs start and stop options.

But my first stumbling block is replacing the mothur formatted RDP training set. What should I be using in its place?

Thank you for your help!

2

I will be working on this too shortly, I will let you know what I come up with!

3

We currently have posted a set of silva.eukarya.* files on the wiki. I’m in the process of updating these but it may be another week or so.

http://www.mothur.org/wiki/Silva_reference_files

Pat