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 4

0.01 3829_BSI_Matsu_MS515F 9067 1423 16 11 7 217

2

Here’s an explanation about why the cutoff is changing in the cluster command, http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F. You can try increasing your cutoff to solve the problem.