Models for estimating the exon inclusion level <i>ψ</i> using the junction reads.

Abstract

<p>(A) The “exon-exon junction model” used by MATS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079448#pone.0079448-Shen1" target="_blank">[11]</a>. Exon 1 and 3 are common exons shared by the two isoforms, and exon 2 is the skipped exon unique for the longer isoform. <i>ψ</i>: exon inclusion level; <i>UJC</i>: number of reads mapped to the upstream junction; <i>DJC</i>: number of reads mapped to the downstream junction; <i>SJC</i>: number of reads mapped to the skipping junction. (B) The “two-isoform model” transformed from (A). The abundances of the longer and shorter isoforms are <i>θ₁</i> and <i>θ₂</i>, respectively, which are estimated using the junction read counts (<i>UJC</i>, <i>DJC</i> and <i>SJC</i>).</p