Filling Gaps between Chimeric junction sites

[mamonster]

Hi,

I was wondering if there is well established method to find the entire transcripts (with exact alternative spliced sequences) formed from the chimeric junctions?
Alignment tools such as STAR and Tophat do provide methods to detect chimeric junction sites from RNA-Seq data. However I couldn't find any obvious solution to assemble the exact isoforms. To be specific, suppose I had a bed file, contains all the potential chimeric junction sites found by the aligners from a RNA-Seq data set(with reference genome), how do I find the exact sequence between the junctions?

Thanks