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Genome Biol. 2013 Mar 28;14(3):R30. doi: 10.1186/gb-2013-14-3-r30.

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.

PMID:
23537109
[PubMed - in process]
PMCID:
PMC4053775
Free PMC Article

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