Many RNA sequencing studies set out to predict mutations, splice junctions or fusion RNAs. Now a team of researchers in France has developed 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.
Availability – CRAC is available at http://crac.gforge.inria.fr.
- Philippe N, Salson M, Commes T, Rivals E. (2013) CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biology 14, R30. [abstract]