alexa TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Pathology

Pathology

Diagnostic Pathology: Open Access

Author(s): Kim D, Salzberg SL

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TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence.

This article was published in Genome Biology and referenced in Diagnostic Pathology: Open Access

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