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Old 01-29-2010, 11:07 AM   #1
DrD2009
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Location: Kansas City

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Default Region Comparison

Hello everyone, I have what I would imagine to be a relatively easy question, but being the bioinformatics newbie I am, I'm unaware of how to proceed.

I have multiple sets of regions of varying sizes specified by chromosome, chromosome start, and chromosome stop. What I would like to do is be able to identify whether or not particular regions from one set overlap with regions from another set. The data is currently in excel.

Any assistance on this would be great.

Thanks in advance.
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Old 01-29-2010, 11:34 AM   #2
mgogol
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Default there are a number of ways

One easy way is using the tools in Galaxy under "Operate on genomic intervals". Just upload both sets of intervals in separate text files, with format like

chr1 tab start tab end

And then you can use intersect, join, or subtract on the intervals.

Last edited by mgogol; 01-29-2010 at 11:38 AM.
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Old 01-29-2010, 12:08 PM   #3
quinlana
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Default

The UCSC Genome Browser's "Table Browser" and BEDTools have this functionality as well. Galaxy is certainly the easiest to use.
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