News
8/11/2013

CRG: Large-scale assessment of transcriptome analysis software

CRG: Large-scale assessment of transcriptome analysis software


News from CRG


CRG and UB researchers have taken part in an international consortium of scientists that has carried out a systematic assessment of gene expression analysis software. The results, which appear in two papers in Nature Methods, may inspire new computing approaches to handle current and future technologies for gene expression analysis and its characterisation.

Scientists use a method called RNA sequencing (RNA-seq) to see how genes are being expressed across an entire genome. But how can they analyse this information, and how good is the software they use to do so? The RNA-seq Genome Annotation Assessment Project (RGASP), an ENCODE-affiliated initiative, evaluated the performance of a wide range of RNA-seq computer programs. They were able to specify which approaches work well for certain tasks, and which areas can be improved.

“To adequately manage sequencing data, we have been working to find new and more-sophisticated alternatives to the currently available methods”, states Roderic Guigó, coordinator of the Bioinformatics and Genomics programme at the Centre for Genomic Regulation in Barcelona. “The conclusions we are presenting in these two papers will help us to extract more information from nucleic acid sequencing methods and facilitate application of these methods to diverse fields such as medicine and biotechnology,” he adds.

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References:
Steijger, T., et al. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods (in press); published online 3 November. DOI: doi:10.1038/nmeth.2714.

Engström, P., et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods (in press); published online 3 November. DOI: doi:10.1038/nmeth.2722.