I'm having a hard time finding information on what exactly the advantage of using the Raw Junction option in TopHat would be. Mostly people just cut and paste the explanation from the TopHat manual. Am I wrong in believing that all this does is take information from one TopHat run and make future runs a little quicker and easier? If that's the case I'm in, but where can I find the BED_to_juncs tool? Doesn't show up in the Tool Shed.