I’ve been trying to classify my OTUs using Silva’s fasta/align files and silva.ncbi taxonomy files but I have faced different problems.
If I want to use the newest Silva release (v_132) I do not have any match between it and the NCBI taxonomy file, since (I presume), sequences’ names are not related between both files. Then, I tried to do the same but using the silva.bacteria.fasta file that is linked from the MiSeqSOP and classifying my OTUs with the same NCBI taxonomy file and I got good results. However, when I looked into the files details I can see that both silva.bacteria.fasta and related NCBI taxonomy file were created in 2012!
Is there any way to know if they are really so old?
And most important, is there any way to use Silva’s v132 release together with a NCBI taxonomic classification file?
Thanks a lot