Basic filtering of candidate gene pairs in SOAPfuse. (a) Duplicated span-reads and junc-reads are removed before calculating the number of supporting reads and only one duplicated read is retained. (b) Genes C and D are adjacent, and they share two exons: exon 4 and exon 5 from Gene C overlap with exon 1 and exon 2 of Gene D, respectively. Span-reads from the overlapped exons are excluded by SOAPfuse. (c) Gene pair M and N has regions with homogenous/similar sequences and reads from these regions are filtered out.