any idea why all sequences are shown in a separate OTU?

Commands in mothur
1

Hello there,

I’m trying to follow the 454 SOP and I have run into a problem when classifying into OTUs. I have a fasta, names and group file and am trying to run ‘dist.seqs’ and then ‘cluster’ on the resulting dist file. When I do this all 18000 sequences are classified into a separate OTU, (giving me 18000 OTUs) and the only cutoff shown is ‘unique’. Does anyone have any tips or ideas about what could be going on?

Thanks
Pavel

2

Check out:

http://www.mothur.org/wiki/Frequently_asked_questions#Why_is_my_dataset_only_clustering_to_.22unique.22.3F
http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F

Pat

3

Ah ok, thanks.