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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