FIGURE 1.

Outline of the methodology for computing gene-level splicing efficiency and specificity. Data for the GAS5 lncRNA in ENCODE RNA-seq data for MCF7 cells are shown. All introns annotated in GENCODE were first considered and those poorly supported by spliced reads were discarded. Among the remaining introns, a nonoverlapping set of introns with the most confident support was selected and used for quantification. The method used for quantifying splicing efficiency and specificity at intron- and gene-level is illustrated at the bottom.