Obtaining exon-intron and intron-exon reads

Question

[fadhil.abubaker]

We're interested in studying the number of reads that start at an exon and "spill" over into the subsequent intron or vice-versa.

We have aligned .bam files and annotation files for h38. What tools/software could we use to get the number of reads from the .bam file that span exon-intron / intron-exon junctions?

[Pierre Lindenbaum]

We have aligned .bam files

how. Which tool ?

[fadhil.abubaker]

We used STAR to get the alignments.

[GenoMax]

Past thread with answers from @Pierre and @Devon: Extracting Intron-Exon Reads from bam files