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 On Dec 7, 2011, at 8:56 AM, Jennifer Jackson 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 > > 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 >> >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support 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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
