Dear all, I ran rMATS on my bams files to detect potential intron retention In my genes.

In the rMATs report I have the IJC (number of reads that mapped to the exon inclusion isoform) numbers for each of my samples. Based on the reported introns by rMATS I also extracted the intron coordinates and calculated the number of reads that mapped to the intron but my numbers (number of reads that mapped to a specific intron) are different (sometimes a big difference) with the IJC values of rMATS for a specific intron. I have not found an explanation for this, could someone please help me to know why there is this difference and how the IJC is exactly calculated?

Thanks you.