Hi,
I am trying to use the new SILVA taxonomy file silva.nr_v119.tax for the classify.seqs command. However, I am not sure what to use as “template” input. Actually, I don’t think I fully understood the purpose of the template file. It used to be the “nogap.bacteria.fasta” for the older version.
classify.seqs(fasta=All_Bac.shhh.trim.unique.good.filter.unique.precluster.pick.fasta, name=All_Bac.shhh.trim.unique.good.filter.unique.precluster.pick.names, group=All_Bac.shhh.good.pick.groups, template=???, taxonomy=silva.nr_v119.tax, cutoff=60, relabund=T, processors=8)
Can anyone help?
Best,
Josephine