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

Vendredi 14 juin 2013, de 14h à 15h30, salle 127, à l'IBC, 95 rue de la Galéra, 34095 Montpellier cedex 5

Présentation:Nicolas PHILIPPE, Institut de Recherche en Biothérapie (IRB), Montpellier, France.                      
 http://www.nicolas-philippe.org/
Titre: CRAC: an integrated approach to the analysis of RNA-seq reads
Résumé :The diversity of cell transcriptomes and the underlying mechanisms remain enigmatic. The RNA-sequencing technique enables us to capture virtually all transcripts produced in cell by obtaining pieces of their sequence, thereby making the transcriptomes diversity amenable to description and investigation. Whatever the biological questions it addresses, each RNA-seq analysis requires a computational prediction of either small scale mutations, insertions deletions, splice junctions or chimeric RNAs. This prediction is currently performed using complex pipelines involving multiple tools for mapping, local coverage computation, and prediction at distinct steps. Here, we propose a novel way of analyzing reads that integrates genomic locations and local coverage, and delivers all abovementioned predictions in a single step. The program CRAC implementing this method, uses a double k-mer profiling approach to detect candidate SNV, indels, splice or chimeric junctions in each single read. Compared to existing tools, CRAC provides state of the art sensitivity and improved precision for all types of predictions, yielding high rates of true positive candidates (99.5 % for splice junctions). When applied to four breast cancer libraries, CRAC recovered 74 % of validated chimeric RNAs and predicted reccurrent chimeric junctions that were overseen by previous studies. Importantly, CRAC improves its predictive performance when supplied with e.g. 200 nt reads and should fit future needs of read analysis.

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Dernière mise à jour le 24/06/2013