[Genome] Retrieving intergenic regions from specific regions on chromosomes

[Travis Ptacek]

I refered to the following link for the method to retrieve intergenic sequence using galaxy:
http://www.soe.ucsc.edu/pipermail/genome/2007-June/013907.html <http://www.soe.ucsc.edu/pipermail/genome/2007-June/013907.html> 
 
I can perform this method sucessfully, but I need to retrieve intergenic sequence from a specific region, not an entire chromosome or genome.
 
When I perform this method using a region of, for example, chr7:115,000,000-116,000,000 using the Known Genes track, Galaxy correctly retrieves information for the known genes in that region. However, when I complement the interval of the query, I get an two huge intervals covering all of chromosome 7 upstream of 115,000,000 and downstream of 116,000,000 in addtion to intergenic regions within chr7:115,000,000-116,000,000. What I want, in this example, are only the intergenic regions within chr7:115,000,000-116,000,000.
 
Thanks in advance,
 
Travis Ptacek