The behavior of this tool is intentional. Regardless of which direction a feature is encoded in, we consider to features having any overlapping DNA to intersect.
However, it would be good for this tool to have an option to handle your use case (only consider intervals overlapping if on the same strand).
On May 5, 2010, at 12:36 PM, Xianjun Dong wrote:
the two forward (+) regions in first query should be onlyintersected with the forward (+) regions in second query, NOT regions on reverse strand. That's my understanding to intersection. Isn't right? From the result, it seems that each region in first query is intersected with each region in second query (NO MATTER its strand). I think if my understanding is correct, this should be correct soon, since intersection is such a widely used tool in Galaxy.