counting junction reads

[muzz56]

I bet someone has asked this question before, but I'll ask it anyway. I have run Tophat and have the accepted hits bam file and the juntions.bed file. I'd like to know the number of reads in the bam file aligning to each junction coordinate in the bed file. I have tried to use bedtools with no success. Does anyone have any idea how to achieve this?. Essentially I'd like to know only the number of reads aligning to junctions.
Regards.

[malcook]

http://malcook-gedanken.blogspot.com/2011/06/tabulating-reads_09.html

[muzz56]

Thanks for the reply. I am just wondering what the input files to this script will be?. Since I'll source the script, I'd like to include the paths to the input files in the script but don't know which inputs are required. R is not my cup of tea so forgive me if this is clear from the script.