Assessment of transcript reconstruction methods for RNA-seq

The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge. We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across…

• WT
  Wellcome Trust

  Award: WT098051
• EM
  European Molecular Biology Laboratory
• NI
  National Institutes of Health
• NH
  National Human Genome Research Institute

  Award: U54HG004555