I'm trying to using snpEff to analyze the effects of SNPs and Indels on yeast protein coding genes. After reading many posts here, I now understand there are very limited options for using snpEff on Galaxy Main. So, I set up a Cloud Instance of Galaxy and loaded the latest version of snpEff (4.0) from the tool shed. Unfortunately, the most recent version of the Saccharomyces cerevisiae reference genome (sacCer3) is not available. In fact, I don't think any S. cerevisiae genome is available. The available genomes can be downloaded using the tool snpEff Download (version 4.0). This tool indicates available genomes can be found at https://snpeff-data.galaxyproject.org/databases/v4_0/. Is it possible to include the sacCer3 reference genome here so that snpEff Download can use it?
I need this as well. thanks
Hello, Galaxy Main (http://usegalaxy.org) is now unlikely to be updated to include this build. However, installing the prior tool version on a local or cloud Galaxy and configuring for this genome is still an option.
Thanks, Jen, Galaxy team