Fig. 2

The regions to search for discordant read pairs are defined by the junction coordinates of the observed fusion transcript. Genomic evidence for a fusion will theoretically be found downstream of the sequences observed on fusion transcript for the 5′ partner and upstream for the 3′ partner, thereby limiting the region needed to search for discordant reads (A). Based on the strand that the fusion partner is located on, the defined search regions change (B). Reads supporting a genomic breakpoint must have a soft-clipped end in an “outie” orientation on the outer read of the pair with respect to the discordant read location (C). Once discordant read pairs supporting a fusion transcript have been identified, we attempt to identify reads with high quality soft-clipped ends that support a genomic breakpoint. Soft-clipped sequences are locally aligned close to the discordant read mate. Note that in this example, each genomic breakpoint is supported by six distinct reads (D)