FIG. 1.

Quantification of percent spliced in for each exon. Overlapping transcripts are used to identify a set of upstream and downstream splice sites, and spliced reads mapping between these and the exon boundaries are counted as inclusion reads (green). Reads mapping directly between the upstream and downstream splice sites are counted as exclusion reads (blue). Reads where one or both ends does not match an annotated splice junction are not counted (gray).