Revised RNA-seq based annotations

To view RNA-seq based annotations at the UCSC browser:

• At UCSC genome browser click on MyData-> TrackHubs -> PublicHubs
• Check "ThorntonHub"
• In the genome browser under "group" look for ThorntonHub. "Andolfatto w501 D. simulans reference assembly" for the current genome release.

New annotations based on RNA-seq data established through Trinity/Augustus annotation pipelines. These transcripts include UTR sequence in addition to intron and exon structures. Many of these annotations have a clear one to one match with CG number Flybase annotations. The remaining genes are labeled according to annotation identifiers based on the Trinity/Augustus annotation pipeline.

Manuscripts using these gene models should cite Rogers et al. 2014 "Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group" publised at G3. Annotations were defined using the D. simulans w501 reference described in Hu et al. 2012.