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Corset: enabling differential gene expression analysis for de novo assembled transcriptomes.

ABSTRACT: Next generation sequencing has made it possible to perform differential gene expression studies in non-model organisms. For these studies, the need for a reference genome is circumvented by performing de novo assembly on the RNA-seq data. However, transcriptome assembly produces a multitude of contigs, which must be clustered into genes prior to differential gene expression detection. Here we present Corset, a method that hierarchically clusters contigs using shared reads and expression, then summarizes read counts to clusters, ready for statistical testing. Using a range of metrics, we demonstrate that Corset out-performs alternative methods. Corset is available from https://code.google.com/p/corset-project/.

SUBMITTER: Davidson NM

PROVIDER: S-EPMC4165373 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Corset: enabling differential gene expression analysis for de novo assembled transcriptomes.

Davidson Nadia M NM Oshlack Alicia A

Genome biology 20140726 7

Next generation sequencing has made it possible to perform differential gene expression studies in non-model organisms. For these studies, the need for a reference genome is circumvented by performing de novo assembly on the RNA-seq data. However, transcriptome assembly produces a multitude of contigs, which must be clustered into genes prior to differential gene expression detection. Here we present Corset, a method that hierarchically clusters contigs using shared reads and expression, then su ...[more]

PMID: 25063469

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