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
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Jennifer Jackson
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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/
