First open Visual studio ..select your project in solution explorer..Right click and choose option "browse with" then set IE as default browser.
Now open IE ..go to
Tools >> Internet option >> Advance>> uncheck the checkbox having "Disable Script Debugging (Internet Explorer).
and then click Apply
and OK
and you are done ..
Now you can set breakpoints in your JS file and then hit the debug button in VS..
EDIT:- For asp.net web application right click on the page which is your startup page(say default.aspx) and perform the same steps. :)
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