Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a powerful method for profiling cancers, but current methods for identifying fusion genes are optimised for short reads. JAFFA (https://github.com/Oshlack/JAFFA/wiki ) is a sensitive fusion detection method that outperforms other methods with reads of 100 bp or greater. JAFFA compares a cancer transcriptome to the reference transcriptome, rather than the genome, where the cancer transcriptome is inferred using long reads directly or by de novo assembling short reads.
CITATION STYLE
Davidson, N. M., Majewski, I. J., & Oshlack, A. (2015). JAFFA: High sensitivity transcriptome-focused fusion gene detection. Genome Medicine, 7(1). https://doi.org/10.1186/s13073-015-0167-x
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