RNA-seq Genome Annotation Assessment Project
The RNA-seq Genome Annotation Assessment Project (RGASP) is designed to evaluate computational methods for RNA-seq data analysis. The primary goals of RGASP are to assess RNA-seq alignment, transcript reconstruction and quantification software, and to determine the feasibility of automated genome annotation based on transcriptome sequencing. RGASP is organized in a consortium framework modeled after the EGASP gene prediction workshop, and several rounds have been conducted to address different aspects of RNA-seq analysis as well as changing sequencing technologies and formats.
Transcript predictions from RNA-seq data have been evaluated against the GENCODE annotation produced as part of the ENCODE project. A total of 25 transcript reconstruction protocols based on 14 programs and pipelines were subjected to a range of metrics for exon identification, isoform assembly and quantification. Promising transcript predictions not covered by GENCODE annotation were validated by experimental methods. These results will be published in a forthcoming paper and additional data will be posted here.
For more information about the RGASP project please check our two publications:
Assessment of transcript reconstruction methods for RNA-seq.
Nature methods 2013;10;12;1177-84
Systematic evaluation of spliced alignment programs for RNA-seq data.
Nature methods 2013;10;12;1185-91