This protocol was so outdated that we decided to remove it.
Please consider using state of the art tools, such as Hisat2 or STAR, if you want to prepare RNA-Seq short read data from gene prediction with AUGUSTUS. Note that BRAKER3 can internally handle the mapping with Hisat2 for you to train GeneMark-ETP and AUGUSTUS, and to predict genes with both pipelines using your extrinsic data.
Contact: augustus-web@uni-greifswald.de