Comparing location of reads mapping to reference genome

[alyamahmoud]

Dear All

I have RNASeq reads of different length (50,100) mapped to the same reference genome. I need to determine if they map to the same regions or different. Which tools do I use ?

I used tophat for the alignment with -g 1 option.

Thanks a lot

[TiborNagy]

I have never heard a tool like this, I think you need to write a scipt.