FusionSeq: Finding Fusions with Paired-End RNA-Seq

We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts such as misalignments or random pairing of transcript fragments and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including 8 cancers with and without known rearrangements.]]> Prostate tissues collected post-robotic prostatectomy surgery and containing high-density tumor areas were used for this study. DNA samples in the study were extracted from tissue and blood, which were collected prior to the prostatectomy surgery.]]>