cluster cutoff problem

Commands in mothur
1

I use mothur 1.33, and when i use cluster command, the cutoff changed to a small number(even with parameter hard=true).
when i set cutoff to 0.03, i only get the unique label, when i set cutoff to 0.10, i can get labels: unique/0.01/0.02/0.03.

mothur > cluster(column=dataset_4444.dat,name=dataset_4433.dat,method=average,cutoff=0.1,hard=true,precision=100)
********************###########
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||||

changed cutoff to 0.0332595

Results:
label numOtus
unique 79527
0.01 39448
0.02 15304
0.03 10731

In the wiki, it says “By default the cutoff parameter is set to cutoff + (5 / (precision * 10.0)).” column parameter is my dist file, and there are distances bigger than 0.15. I want to know how the cutoff changed itself?

2

You might want to check out this post…
http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F

3

Thank you very much.

4

I don’t completely understand why the cutoff changes after reading the above FAQ (http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F).

Can you explain: “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, because it’s not possible to merge at a higher level and keep all the data” in more detail? Why do you “lose data” when you start clustering at higher cutoff levels?

I am trying to create OTUs at multiple different sequence dissimilarity thresholds, from 0.00 to 0.25 at 0.01 (1%) increments. When I try and set the cutoff to 0.25 using the cluster command, it always changes the cutoff to 0.14. Is it possible to do what I am trying to do here (create OTUs with dissimilarity thresholds up to 30%)?

Thanks!

5

Please post this question to a new thread, the original thread is more than a year old.

Pat