change in clustering cutoff

Commands in mothur
1

Hi,

I am trying to cluster my sequence dataset with a cutoff of 0.03. the dist.seqs ran to success when this cutoff was set. however when I run the cluster command, the cutoff is automatically reset to 0.01. Does this change happens with respect to the dataset? I want my dataset to be clustered at 97% identity in order to determine the number of OTUs. The log file report is below.

mothur > cluster(column=samples_contigs.unique.good.filter.unique.precluster.pick.dist, count=samples_contigs.unique.good.filter.unique.precluster.pick.count_table)
********************###########
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

changed cutoff to 0.0118322

Output File Names:
samples_contigs.unique.good.filter.unique.precluster.pick.an.unique_list.list

It took 2180 seconds to cluster

2

Check this out and let us know if you have questions…

http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F

3

Thanks for your response. I just went through your FAQ section. I just have a query!!

When I set a cutoff to 0.05 in my dist.seqs run, hw do I get a pair that has more distance as my result(as per the FAQ-Let’s say you set the cutoff to 0.05. If one cell has a distance of 0.03 and the cell it is getting merged with has a distance above 0.05 then the cutoff is reset to 0.03).

Am i missing something here!!!

4

Use a cutoff of 0.15 in dist.seqs like we do in the SOPs