The Drosophila genome has been updated to dm6. However, the Galaxy still only use dm3. Many gene annotations has been changed which caused a lot of headaches for figuring out the genes associated with particular ChIP-Seq peaks. Can someone update that in the Galaxy? I know how to map that ChIP-Seq data with custom genome, but all the tools such as bedgraph/bigwig still require a reference genome. Thanks.
Updating reference genomes on http://usegalaxy.org is a priority. Meanwhile, a Custom reference genome can be used with most tools. For those few tools that interpret the "database" attribute, create a Custom Build and assign that to the input datasets.
Best, Jen, Galaxy team