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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