I am using RNASeq data to improve genome annotations of a non model organism. The so called hints for augustus can be extracted from the bam files and my question is about using 2-pass or not because the lack of annotations (--sjdbGTFfile).
The manual says: "Using annotations is recommended either a the genome generation step, or mapping step."
Is it advisable that I proceed with 1-pass only? I gave 2-pass a try for a few samples and it seems to improve the overall results.
Sorry if I have missed this information elsewhere and thanks for the amazing job.
All the best,