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bioRxiv · 10.1101/013698

JAFFA: High sensitivity transcriptome-focused fusion gene detection.

Nadia M Davidson·Ian J Majewski·Alicia Oshlack
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Abstract

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 optimized for short reads. JAFFA (https://code.google.com/p/jaffa-project/) is a sensitive fusion detection method that clearly out-performs other methods with reads of 100bp 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.

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Nadia M Davidson, Ian J Majewski, Alicia Oshlack. 2015-01-12. JAFFA: High sensitivity transcriptome-focused fusion gene detection.. https://doi.org/10.1101/013698

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