Hi,
I am a very beginner user trying to go through the MiSeq_SOP tutorial and when I try to execute
chimera.vsearch(fasta=stability.trim.contigs.good.unique.good.filter.nique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)
I get the error: Invalid command.
Valid commands are: align.check,align.seqs,amova,anosim,bin.seqs,catchall,chimera.bellerophon,chimera.ccode,chimera.check,chimera.perseus,chimera.pintail,chimera.slayer,chimera.uchime,chop.seqs,classify.otu,classify.rf,classify.seqs,classify.svm,classify.tree,clear.memory,clearcut,cluster,cluster.classic,cluster.fragments,cluster.split,collect.shared,collect.single,consensus.seqs,cooccurrence,corr.axes,count.groups,count.seqs,create.database,degap.seqs,deunique.seqs,deunique.tree,dist.seqs,dist.shared,fastq.info,filter.seqs,filter.shared,get.commandinfo,get.communitytype,get.coremicrobiome,get.current,get.dists,get.group,get.groups,get.label,get.lineage,get.mimarkspackage,get.otulabels,get.otulist,get.oturep,get.otus,get.rabund,get.relabund,get.sabund,get.seqs,get.sharedseqs,hcluster,heatmap.bin,heatmap.sim,help,homova,indicator,kruskal.wallis,lefse,libshuff,list.otulabels,list.seqs,load.logfile,make.biom,make.contigs,make.fastq,make.group,make.lefse,make.lookup,make.shared,make.sra,make.table,mantel,merge.files,merge.groups,merge.sfffiles,merge.taxsummary,metastats,mgcluster,mimarks.attributes,nmds,normalize.shared,otu.association,otu.hierarchy,pairwise.seqs,parse.list,parsimony,pca,pcoa,pcr.seqs,phylo.diversity,phylotype,pipeline.pds,pre.cluster,primer.design,quit,rarefaction.shared,rarefaction.single,remove.dists,remove.groups,remove.lineage,remove.otulabels,remove.otus,remove.rare,remove.seqs,rename.seqs,reverse.seqs,screen.seqs,sens.spec,seq.error,set.current,set.dir,set.logfile,sff.multiple,sffinfo,shhh.flows,shhh.seqs,sort.seqs,sparcc,split.abund,split.groups,sub.sample,summary.qual,summary.seqs,summary.shared,summary.single,summary.tax,system,tree.shared,trim.flows,trim.seqs,unifrac.unweighted,unifrac.weighted,unique.seqs,venn.
Why isn't chimera.vsearch listed as a "valid command"? Am I missing something? I am following the tutorial word-for-word with the data provided in the tutorial.