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deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

Figure 2

Conditions for considering two paired end reads to have originated from the same fusion transcript.

a) Fusion transcript X-Y supported by a paired end read spanning the fusion boundary. b) Discordant paired end reads represent reads potentially spanning a fusion boundary. Each discordant alignment suggests fusion boundaries in the regions adjacent to the alignments in each transcript. The fusion boundary region, shown in gray, is the region in which we expect a fusion boundary to occur. c) The overlapping boundary region condition is the condition that the fusion boundary regions in each transcript must overlap. d) The difference between the fragment lengths of two paired end reads spanning a fusion boundary is . e) The similar fragment length condition is the constraint that must be no more than .

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1001138.g002