Hello Vinny,

The tool "Text Manipulation -> Select random lines from a file" may be of interest to you. This will not generate random intervals, but it can select random lines from an interval file or any other file.


The ENCODE tool as build specifically on the target genomes using external files. This tool may be generalized at some point in the future, but right now there are no current plans to do so.

Hopefully the random line tool will be useful or you will be able to locate an alternative,

Best,

Jen
Galaxy team

On 11/29/11 12:43 PM, Vincent Joseph Lynch wrote:
To Whom It May Concern,

I am curious if there is a tool within Galaxy to generate a set of
random intervals from a particular genome similar to the "Random
Intervals" tool within the ENCODE tools? I am using the "Aggregate
datapoints" tool to get phastCons conservation scores for peaks from
ChIP-Seq data. I would like to compare these scores to a random
expectation so would like to be able to use a Random Intervals-like tool
to generate a set of random positions to compare to the experimental set.

Best,
Vinny




Vincent J. Lynch, Associate Research Scientist
Department of Ecology and Evolutionary Biology & Yale Systems Biology
Institute
Yale University

"There is a grandeur in this view of life, with its several powers,
having been originally breathed into a few forms or into one; and that
whilst this planet has gone on cycling according to the fixed laws of
gravity, from so simple a beginning endless forms most beautiful and most
wonderful have been, and are being, evolved." -C. Darwin, 1859



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