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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim*, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley and Steven L Salzberg

Genome Biology 2013, 14:R36  doi:10.1186/gb-2013-14-4-r36

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http://genomebiology.com/2013/14/4/R36
gb-2013-14-4-r36