I have worked through the mothur SOP, and am now starting to process my own data. I am wondering what parts of the SOP code I need to modify. Here are a few things I have questions about:
pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=8)
–>First, what exactly is the silva.bacteria.fasta file? Second, the SOP states that you should use the updated SILVA reference files. Does this mean I should find an updated version of the silva.bacteria.fasta file? If so, where do I find that?
classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)
–>what exactly are the trainset9_032012.pds.fasta and trainset9_032012.pds.tax files? I am assuming I should also get updated versions of these two files. Where do I find them?
Is there anything else in the SOP that needs to be updated or modified when working with your own data?