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TrinityFusion leverages chimeric and unmapped reads to assemble fusion transcripts and transcripts of likely foreign origin (microbes and viruses), as a way of facilitating analysis of cancer transcriptomes.
TrinityFusion performs de novo transcriptome assembly from RNA-seq data using Trinity, and uses GMAP to identify candidate fusion transcripts. Bowtie2 is finally used to capture the reads that support the fusion, and fusion candidates are filtered according to evidence support and characteristics of the fusion gene partners. An overview of the process is illustrated below:
