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.

Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigó R, Harrow J and Bertone P

Nature methods 2013;10;12;1177-84

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P and RGASP Consortium

Nature methods 2013;10;12;1185-91