Since retained introns can't be measured by junctions alone, use the exon-intron boundary reads in addition to the junctions to measure the co-incidence of splicing. I saw this equation in some paper somewhere and now I can't find it. I swear it was called "co-incidence of splicing metric" but that doesn't turn up anything useful in Google (vanilla) or Google Scholar.
Since retained introns can't be measured by junctions alone, use the exon-intron boundary reads in addition to the junctions to measure the co-incidence of splicing. I saw this equation in some paper somewhere and now I can't find it. I swear it was called "co-incidence of splicing metric" but that doesn't turn up anything useful in Google (vanilla) or Google Scholar.