I am running mothur using silva 132. I downloaded the following files from both silva and rdp to run the program. I feel like some files are missing; can anyone check and let me know if I am missing something? I could not see fasta files when I downloaded the silva files version 132.
Files in the Silva folder
Files added to my fasta files
Hello!
The files you use depend on the type of analysis you want to do.
If your intention is to follow the Mothur SOP without modifications, you would be missing the ‘silva.bacteria.fasta’ file. You can find this here: MiSeq SOP
Also, I would use the latest version of the datasets, and you can find the Mothur-compatible versions here Silva reference files and here RDP reference files.
But again, your database should align with your objective, as other databases are tailored for specific objectives (e.g., PR2 for eukaryotes or CyanoSeq for cyanobacteria).
I hope this helps. Good luck! 
