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

Genome Biology
Nadia M Davidson, Alicia Oshlack

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/.

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Dec 16, 2017·MSphere·Louisi Souza de OliveiraFabiano L Thompson
May 21, 2019·Genome Biology and Evolution·Zhenhua ZhangBojian Zhong
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Datasets Mentioned

BETA
SRR453566

Methods Mentioned

BETA
RNA-seq

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