We did not get the right information what we are looking for. The only class codes after Cuffcompare and Cuffmerge we get is "=" and "j". Other Class codes which are "o", "i", "s", "x" are missing after analysis. Can you please let us know if Cufflinks from Galaxy only selects the class code is "=" and "j" and not others?
Tool name: Cuffcompare
Tool version: 0.0.6
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/0.0.6
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/cuffcompare