Hi all,
I've been given a set of **RNA-Seq** fastqs (4 samples) and a collaborator would like to know how many defined **intron-exon** junction in his favorite gene are detected in those reads.

My idea was to clean the reads with cutadapt, align with Bowtie and create a custom program to loop over  the cigar string and detecting the junctions.

or is there an existing tool for this ? 
Bonus if the tool can tell me wether two junctions belong to the same transcript.
If you use the STAR aligner, it will output `SJ.out.tab` with high confidence collapsed splice junctions in tab-delimited format.