Given a bam file, obtain read numbers that traverse a specific exon junction

Question

[oriolebaltimore]

Hello group,

I have a list of exons from several genes that are differentially spliced between two conditions.

I want to identify if these exons are spliced in another set of 50 BAM files (that include two condition 25 per each). Typically one can run MISO or mats for this kind of analysis. I am not interested in running MISO or BAM.

I just want to count read numbers that traverse the exon junction from my list.

BAM files are generated using STAR alignment.

Is there way I can find junction read numbers for each BAM file (I dont have a gtf or bed file that is obtained as result of running tophat/cufflinks).

Thanks Adrian