<p>After removing reads that have full-length alignments to the genome, reads are divided in half and aligned to the genome (step 1 as defined in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013875#s4" target="_blank">Materials and Methods</a>). The HMM is trained using a subset of the read-half alignments (step 2a). The HMM bins quality scores into five levels. Although only three levels are shown in this overview for simplification, the values for all five levels can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013875#pone-0013875-t001" target="_blank">Table 1</a>. The trained HMM is then used to determine the splice position within each read-half alignment (step 2b). The remaining second piece of the read is then matched downstream to find the other intron edge (step 3). The initial set of splice junctions then proceed to rescue (step 4) and filter and collapse (step 5) to generate the final set of splice junctions.</p
