I would like to use the SILVA 123 database to classify my OTUs. So far I have only been able to use RDP to classify my OTUs and I saw that the only SILVA files available in MOTHUR are for alignment. Is is possible to use the SILVA 123 database to classify OTUs and not only for alignment?
Yes, you can use the same files (the alignment and also the tax file) for the classifying step.
Thank you very much Leo,
I guess my problem is that I do not know what file should I use as reference when performing classify.seqs. In the past I have used rdp as a database and there is a fasta file to use as reference. What file should I use as reference when using the silva 123 database? Should I use silva.nr_v123.align?
Yes, that is the “fasta” (well, it is actually a fasta : ) ). So, that is the “reference= silva.nr_v123.align”; then “taxonomy=” should be the .tax file with the same name (silva.nr_v123.tax? maybe?).
I assume you are using the mothur-formatted silva? https://mothur.org/wiki/silva_reference_files/
Out of curiosity, why are you using the 123 and not the last 138?
It worked! Now I have more OTUs classified than before. I’m using 123 because in this paper the authors worked with rumen samples (like me) and they addressed the issue of low OTU classification. They improved taxonomy assignment and introduced the modifications in SILVA 123. Would you recommend me to use SILVA 138 because it’s more updated? I could try, it’s just that I don’t know if it will work well for the rumen samples.
Well, actually, 138_1 was better than 123. Thank you very much Leo.