#Annotation methods

This repo contains scripts, etc., that we use for RNA-seq based genome annotations. The repo also serves as supplementary material for this paper:

• Rogers, R. L., L. Shao, J. Sanjak, P. Andolfatto and K. R. Thornton (Accepted) Sex-biased expression in the Drosophila melanogaster group. G3: Genes, Genomes, Genetics. Abstract

The Trinity_with_norm folder contains the script for how we ran Trinity in the above paper.

The Augustus folder contains how we ran blat + Augustus to generate "hint-guided" annotations for each genome. The files also include some editorializing on installing blat, which can be quite tricky.

##Future-proofing

In the case of future modification of these scripts, I have released version 0.1.0 of this repository to correspond to the command lines used in Rogers et al.