Thanks for explaining! Then our tutorials and workflows will likely work for you! The first two hands-on items have full materials to walk you through the steps.
Once you are comfortable with the basic path, you can consider these IWC workflows. These can be adjusted to accept a custom reference genome as needed. All annotation will need to be sourced from public repositories.
If you don’t have your reference data yet, this is how to get genome data from NCBI into Galaxy But you can use any source that you want and process will be the same! Please ask if you have questions.
If the analysis is new to you, starting with the tutorial version will be easier since these cover what is happening at each step and why, and each has a video with more.
If you species doesn’t have a reference genome, you can also explore tools like Salmon for transcriptomic analysis. We have some help in topics tagged with salmon but there isn’t a tutorial. The assembly and annotation would be predictive and non-trivial. Locating a publication would be the first step, then you could adapt that to a Galaxy protocol.
Hope this helps! 