@article{Steijger.2013.24185837,
  author = {Steijger, T and Abril, JF and Engström, PG and Kokocinski, F and The RGASP Consortium and Abril, JF and Akerman, M and Alioto, T and Ambrosini, G and Antonarakis, SE and Behr, J and Bertone, PBohnert, R and Bucher, P and Cloonan, N and Derrien, T and Djebali, S and Du, J and Dudoit, S and Engström, PG and Gerstein, M and Gingeras, TR and Gonzalez, D and Grimmond, SM and Guigó, R and Habegger, L and Harrow, J and Hubbard, TJ and Iseli, C and Jean, G and Kahles, A and Kokocinski, F and Lagarde, J and Leng, J and Lefebvre, G and Lewis, S and Mortazavi, A and Niermann, P and Rätsch, G and Reymond, A and Ribeca, P and Richard, H and Rougemont, J and Rozowsky, J and Sammeth, M and Sboner, A and Schulz, MH and Searle, SM and Solorzano, ND and Solovyev, V and Stanke, M and Steijger, T and Stevenson, BJ and Stockinger, H and Valsesia, A and Weese, D and White, S and Wold, BJ and Wu, J and Wu, TD and Zeller, G and Zerbino, D and Zhang, MQ and Hubbard, TJ and Guigó, R and Harrow, J and Bertone, P},
  title = {{Assessment of transcript reconstruction methods for RNA-seq}},
  journal = {Nature methods},
  pages = {},
  year = {2013},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/24185837},
  abstract = {{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 methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.}}
}