Obtaining fused regions by two methods. A junction sequence in a fusion transcript from a gene pair, Gene A and Gene B, in blue and orange, respectively, is shown. The junction site is displayed as yellow round dots on the fusion sequence. (a) Two unmapped reads (candidate junc-reads) are shown around the fusion sequence. Each read is bisected into two isometric HUM reads: one HUM can map to one gene of the pair, while the other one cannot map to the gene as it covers the junction site (yellow round dot). From the location of the mapped HUM read, SOAPfuse extends one HUM read-length to obtain the fused region, in which the junction site is located (yellow triangle). (b) Span-read mapping to the gene pair is shown. End 1 maps to Gene A (with position MP1), and end 2 maps to Gene B (with position MP2). From the mapped positions of both ends, SOAPfuse determines the potential fused region based on insert sizes (INS), standard deviation of insert sizes (SD), and the length of reads (RL1 and RL2 for both ends, respectively) and extends proper flanking bases to obtain the fused region.