Aligning reads to genome/transcriptome

Question

[EVR]

Hi all, I have a RNAseq data and I am interested in only those reads which maps to the exactly between two scaffolds or transcripts. I mean if a RNA read is of length 50 and it aligned to a scaffold or transcript with one part of it aligned to one end of a scaffold/trancsript and other part to a one end of other scaffold. Is there to coerce the aligner like bowtie or tophat to map such kind of reads that align towards end of scaffolds/transcripts. Kindly guide me. Thanks in advance

[GenoMax]

There is no need to coerce an aligner as long as it is splice aware. You could align normally and then look for alignments than span two scaffolds.Something like: What Is The Most Direct Way To Extract The Splice Junctions From A Sam File?

[EVR]

I used Tophat which is a splice aware. My concern is that whether the reads which clinging between two scaffolds will be discarded due to seed length or is there is way to specify to retain the reads that clings between two scaffolds. Also splice junction is usually found within a scaffold but here its between scaffolds