Region Comparison

[DrD2009]

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.

[mgogol]

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.

[quinlana]

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