TY - JOUR AU - Philippe, Nicolas AU - Salson, Mikaël AU - Commes, Thérèse AU - Rivals, Eric PY - 2013 DA - 2013/03/28 TI - CRAC: an integrated approach to the analysis of RNA-seq reads JO - Genome Biology SP - R30 VL - 14 IS - 3 AB - 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. SN - 1474-760X UR - https://doi.org/10.1186/gb-2013-14-3-r30 DO - 10.1186/gb-2013-14-3-r30 ID - Philippe2013 ER -