This method addresses the problem of how to use RNA-Seq data for transcriptome reconstruction and quantification, as well as novel transcript discovery in partially annotated genomes. Researchers at Georgia State University have developed a novel annotation-guided general framework for transcriptome discovery, reconstruction and quantification in partially annotated genomes and compared it with existing annotation-guided and genome-guided transcriptome assembly methods. Their method, referred as Discovery and Reconstruction of Unannotated Transcripts (DRUT), can be used to enhance existing transcriptome assemblers, such as Cufflinks, as well as to accurately estimate the transcript frequencies. Empirical analysis on synthetic datasets confirms that Cufflinks enhanced by DRUT has superior quality of reconstruction and frequency estimation of transcripts.
The software is written in C++ and is available at: http://www.cs.gsu.edu/~serghei/?q=drut
- Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A. (2012) Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. In Silico Biol 11(5):251-61. [abstract]