Dear Galaxy team,
Thank you very much for your reply for the last 2 posts. Currently, we get only "=" and "j" class codes with Cuffcompare and Cuffmerge and followed with Cuffdiff analysis. We would like to get an early response for this problem.
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