Random Intervals ?

Question: Random Intervals ?

7.0 years ago by

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

chip-seq • 773 views

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modified 7.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.0 years ago by Vincent Joseph Lynch • 40

7.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, Thanks for getting back to me. I'm not sure whether selecting random lines will work but will give it a try. If such a tool is ever built in the future it would be nice if it could match a file that has empirical data to generate a null expectation. For example, I have a bed file with the location of features that are of variable length and these features tend to be associated with particular genes. So randomly sampling the genome n times equal to the feature length from the original bed file should give some idea of a random expectation for the association of the feature (ChIp-Seq peaks or the like) with other features (genes or the like). Thanks again for the quick reply! 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

ADD REPLY • link written 7.0 years ago by Vincent Joseph Lynch • 40

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