Question: calculating Unifrac significance with more than 10 samples
gravatar for mr.ray.keren
4.4 years ago by
European Union
mr.ray.keren0 wrote:

The max number of samples (categories) that can be used in the Unifrac Significance tool is 10 since the max permutations are 1000.

Is there a way to overcome it since I have over 10 samples?


galaxy • 839 views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by mr.ray.keren0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This is from the tool version included in the Tool Shed repository "mothur_toolsuite"?

If so, the parameter "iters - Number of iterations to try (default 1000):" is a variable and can be modified. Expected impact on performance can be researched in the underlying source tool documentation or by testing. Specific inputs will almost certainly be a factor. Scale up resources as necessary, if possible (when using a CloudMan or local Galaxy), being aware that not all computations scale well (some jobs become exponentially large and unable to run at a satisfactory rate, or at all, under any configuration).

If you are using this tool at a a public Galaxy site (it is not on the Main Galaxy instance at, then it could be that this has been hard-set by the administrators of the instance. You could contact them about it (contact information is generally on the middle splash page of the browser), but I suspect that moving to your own cloud Galaxy might be necessary in a case such as this.

Hopefully this leads to a solution, Jen, Galaxy team

ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k

Thanks! The mail was lost in the inbox. I contacted the Galaxy administrators and they advised that I don't do each pair comparison with their software because with more samples I might get significant values just by chance.

ADD REPLYlink written 4.3 years ago by mr.ray.keren0
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