Predicting Genes with AUGUSTUS and RNA-Seq Data

RNA-Seq data has the potential to improve the accuracy of structural gene prediction in eukaryotes. It was recently shown that the gene prediction tool AUGUSTUS [1] is able to reach a superior gene detection sensitivity (i.e. all intron-exon-borders of protein coding regions are correct) when combined with RNA-Seq data [2]. Here, we present workflows and instructions for predicting genes with AUGUSTUS and RNA-Seq data.

[1] M. Stanke, M. Diekhans, R. Baertsch, D. Haussler (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
Bioinformatics, 24(5):637

[2] T. Steijger, J.F. Abril, P.G. Engström, F. Kokocinski, The RGASP Consortium, T.J. Hubbard, R. Guigó, J. Harrow & P. Bertone (2013) Assessment of transcript reconstruction methods for RNA-seq.
Nature Methods, doi:10.1038/nmeth.2714