Hi Galaxy Team:
Rice genome has 12 chromosomes. But our output file from Tophat2 is only containing Chr1 to Chr9. We would like to know data alignment for Chr10 to Chr12 is missing.
We use the same dataset to run Cufflinks and Cuffdiff tools. But we get only "j" and "=" class code. Can you please explain why we are missing rest of the class codes (e.g.: x, o, s, i etc).
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