Additional file 11.

Figure S2 - Finding fusions using two segments and partner reads in paired-end reads. (a) TopHat allows one to three mismatches when mapping segments using Bowtie, which enables segments to be mapped even if a few bases cross a fusion point (the last two bases of the red segment, GG). These two segments, mapped to two different chromosomes, are used to identify a fusion point. (b) For paired-end reads, the mapped position of the partner read is used to narrow down the range of a fusion point. The second segment (shown in green) cannot be mapped because it spans a fusion point. Here, its partner read is mapped and the fusion point is likely to be located within the inner mate distance ± standard deviation of the left genomic coordinate of the partner read. TopHat-Fusion is able to use this relatively small range to efficiently map the right part of the second segment to the right side of a fusion (case 2). The left part of the second segment is aligned to the right side of the mapped first segment (case 3).

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Kim and Salzberg Genome Biology 2011 12:R72   doi:10.1186/gb-2011-12-8-r72