I am new to Galaxy (which is great, thanks!) and I would like to use Tophat2 with chicken data. Unfortunately galgal4 (and other previous chicken genomes) are not in the built-in dropbox - unlike with Tophat 1.5.
I looked on the forums etc. but it is still no clear to me how I should proceed if I still want to use Tophat2. What is the correct exact procedure to import my genome galgal4 such I could use it in Tophat but also later for some differential expression?
Thank you for your help.
Tool name: Tophat2
Tool version: 0.6
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/tophat2