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Genome Biol. 2014 Jul 26;15(7):410. doi: 10.1186/s13059-014-0410-6.

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/.

PMID:
25063469
PMCID:
PMC4165373
DOI:
10.1186/s13059-014-0410-6
[Indexed for MEDLINE]
Free PMC Article

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