Dear Galaxy Help,

I was wondering if it would be possible to get the coordinates that caused the merge as the output from "Tools: Operate on Genomic Intervals: Merge the overlapping intervals of a query", rather than the entire merged interval as the output.  Kind of like the output from "Intersect: Overlapping Pieces of intervals" option, which returns the exact base pair overlap between two queries.  It might be helpful in some cases to see only the coordinates that caused the merge.  From my limited Galaxy knowledge, by using the "Intersect" option and comparing a file to itself, the output would also include those complete overlaps of interval_1 in file1 to it's copy interval_1 in file2.  If there is already a way to get just the coordinates that caused the merge, I would be interested to learn more.  

Thanks again for your help!
- Erika 

E.M. Kvikstad
Academic Computing Fellow
IGDP Genetics
Center for Comparative Genomics and Bioinformatics 
The Pennsylvania State University
208 Mueller Lab
University Park, PA 16802
(814) 863-2185