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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.

SUBMITTER: Philippe N 

PROVIDER: S-EPMC4053775 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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

Philippe Nicolas N   Salson Mikaël M   Commes Thérèse T   Rivals Eric E  

Genome biology 20130328 3

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. Impo  ...[more]

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