RNA-Seq differential expression analysis: An extended review and a software tool

The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High-throughput transcriptome sequencing (RNA-Seq) has become the main option for these studies. Thus, the number of methods and softwares for differential expression analysis from RNA-Seq data also increased rapidly. However, there is no consensus about the most appropriate pipeline or protocol for identifying differentially expressed genes from RNA-Seq data. This work presents an extended review on the topic that includes the evaluation of six methods of mapping reads, including pseudo-alignment and quasi-mapping and nine methods of differential expression…

• CD
  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
• CN
  Conselho Nacional de Desenvolvimento Científico e Tecnológico

  Award: 406099/2016-2
• FA
  Fundação Araucária

  Award: 340/2014