Unknown

Dataset Information

0

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

Json Xml
altmetric image

Publications

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]

Similar Datasets

Unknown An Integrated Approach for RNA-seq Data Normalization.
| S-EPMC4924883 | biostudies-literature
Unknown Local sequence and sequencing depth dependent accuracy of RNA-seq reads.
| S-EPMC5550947 | biostudies-other
Unknown HLA typing from RNA-Seq sequence reads.
| S-EPMC4064318 | biostudies-literature
Unknown TransMeta simultaneously assembles multisample RNA-seq reads.
| S-EPMC9341511 | biostudies-literature
Unknown Targeted variant detection using unaligned RNA-Seq reads.
| S-EPMC6701478 | biostudies-literature
Unknown Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis.
| S-EPMC5133374 | biostudies-literature
Unknown Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression.
| S-EPMC6022640 | biostudies-literature
Unknown SCell: integrated analysis of single-cell RNA-seq data.
| S-EPMC4937196 | biostudies-literature
Unknown JAGuaR: junction alignments to genome for RNA-seq reads.
| S-EPMC4111418 | biostudies-literature
Unknown Shark: fishing relevant reads in an RNA-Seq sample.
| S-EPMC8088329 | biostudies-literature