I have claasify otu file but now i need to run asv command but that command need asv list so how can i use that list because in mothur i dont have that list so now how can i run that command to get asv from classify otus please help me regarding this , (rpoB.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.subsample.fn.unique_list.list) that list i have so using this how can i run asv command.
classify.otu(list=rpoB.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.subsample.fn.unique_list.asv.list, count=rpoB.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.pick.subsample.count_table, taxonomy=rpoB.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.subsample.fn.unique_list.0.021.cons.taxonomy, label=ASV)
Hi there,
I’d encourage you to follow along with the MiSeq SOP section on ASVs. You’ll want to run two commands with your data that will look something like this…
mothur > make.shared(count=rpoB.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.pick.count_table)
mothur > classify.otu(list=rpoB.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.asv.list, count=rpoB.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.pick.count_table, taxonomy=rpoB.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.taxonomy, label=ASV)
I wouldn’t recommend subsampling the ASVs until after you have constructed the shared file.
Pat