Figure 1

Schematic outline of GLiMMPS. (a) RNA-seq reads mapped to splice junctions of alternatively spliced exons are used for estimating exon inclusion levels ψ. Shown here is a schematic illustration using the skipped exon (SE) type of alternative splicing events as the example. White, sQTL target exon; black and gray, flanking exons. The inclusion junction (IJ) reads consist of reads mapped to the upstream and downstream splice junctions of the exon inclusion isoform, while the skipping junction (SJ) reads are reads mapped to the skipping splice junction of the exon skipping isoform. (b) Illustration of the GLiMMPS statistical model. SNP genotype effect is modeled as fixed effect β _j . The overdispersion is modeled as individual level random effect $u_{ij}$.