Hello Eric,

I am not sure if you have already explored the other tools in this same tool group or not, but if you haven't, the tool " Cluster the intervals of a dataset" may be what you are looking for. Help/graphics for usage is on the tool form itself. Note that the coordinates would not be strictly for the "overlapping" base regions only, but that there are some output alternatives.

Protocol 4 from this publication also contains a review and example usage tutorial for interval operation tools:
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

Often one tool does not fit all cases, and a combination of tools is best. For example, if you just wanted coordinates for the overlapping portions (including the specified "distance"), perhaps start by using a tool like "Get flanks", set your desired distance and base off the peaks, merge the result back with the peaks to create the query interval sets, then intersect those extended peaks. This is just a general idea of how to string together tools - other/additional manipulations may be needed to create a complete workflow to meet your exact goals.

Take care,

Jen
Galaxy team

On 3/29/13 1:30 PM, Eric Van Otterloo wrote:

Hello -

I have been trying to find a solution to identify overlapping peaks between two ChIP-Seq datasets. I have used the "Intersect the intervals of two datasets" function, under the Operate on Genomic Intervals toolset - however, I would like to be able to specify a given distance between the peaks to still be counted as "overlapping", and this tool requires at least 1bp overlap between peaks to be counted. For example, even if two peaks are within 500bp of each other (but don't overlap) I would like to score this as overlapping and get the resulting genomic coordinates for downstream analysis.

Thanks in advance for your help!

Eric Van Otterloo
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