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Journal Articles Genome Biology Year : 2013

CRAC: an integrated approach to the analysis of RNA-seq reads

Abstract

A large number of RNA-sequencing studies set out to predict mutations, splice junctions or fusion RNAs. We propose a method, CRAC, that integrates genomic locations and local coverage to enable such predictions to be made directly from RNA-seq read analysis. A k-mer profiling approach detects candidate mutations, indels and splice or chimeric junctions in each single read. CRAC increases precision compared with existing tools, reaching 99:5% for splice junctions, without losing sensitivity. Importantly, CRAC predictions improve with read length. In cancer libraries, CRAC recovered 74% of validated fusion RNAs and predicted novel recurrent chimeric junctions. CRAC is available at http://crac.gforge.inria.fr.
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Dates and versions

inserm-00850972 , version 1 (10-08-2013)

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Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals. CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biology, 2013, 14 (3), pp.R30. ⟨10.1186/gb-2013-14-3-r30⟩. ⟨inserm-00850972⟩
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