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Old 03-30-2013, 03:00 AM   #1
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Default RNA-Seq: CRAC: an integrated approach to the analysis of RNA-seq reads.

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

Genome Biol. 2013 Mar 28;14(3):R30

Authors: Philippe N, Salson M, Commes T, Rivals E

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 - as supplied by publisher]



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