clustered with 0.03.. out put returned 0.01

Commands in mothur
1

Hi there,

When running:

mothur > dist.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, cutoff=0.20)
mothur > cluster(column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.dist, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.pick.count_table)
mothur > make.shared(list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.pick.count_table, label=0.03)
mothur > rarefaction.single(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.shared)

I generated: 0.01 instead of 0.03

label Group numOtus Otu0001 Otu0002 Otu0003
0.01 3829_2F_MS515F 9067 1 0 0

0.01 3829_BSI_Matsu_MS515F 9067 1423 16 11


Can you tell me what I may be doing wrong? I was expecting my labels to be 0.03

Thanks,

Amanda Sapp

2

You likely need to use a larger cutoff in dist.seqs. Can you try replacing dist.seqs/cluster with cluster.split and use cutoff=0.25?

Pat