Obtaining exon-intron and intron-exon reads
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?
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how. Which tool ?
We used STAR to get the alignments.
Past thread with answers from @Pierre and @Devon: Extracting Intron-Exon Reads from bam files