Hello Ujani, There are two options with the "Operate on Genomic Intervals -> Intersect" tool. One is 'Overlapping Intervals' and the other is 'Overlapping pieces of Intervals'. The file order does matter very much for the first choice with respect to the intervals themselves. And if there are any other fields in your data, the file order will matter with both (any additional fields in the first file are carried through to the output). These operations are explained in detail with graphics on the tool form itself. Please give this another try and let us know if you have more questions, Jen Galaxy team On 10/12/12 11:26 AM, FNU Ujani Chakraborty wrote:

Hi! I was trying to intersect two data sets yesterday and today....and it seems like in the dialog box that asks me to enter the names of the 2 datasets that I wish to intersect, the order in which I list the two datasets makes a difference and gives me different number of overlaps. So if I have two datasets A and B if I enter A first and B second in the dialog box, the result is different from if I enter B first and A second in the dialog box. I dont understand how this is possible, since the overlap should not depend on the order of the entries. Am I doing or understanding something wrong?

Any help will be appreciated! Ujani

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