6 days ago by
The tools in the group NGS: RNA Analysis at Galaxy Main (http://usegalaxy.org) include a few software packages for differential expression analysis. I am fairly certain that none of these work with this particular input file format directly. Processing the counts with the tools provided in Galaxy from sorted BAM alignment data files (and often reference data) is how to prepare and process the data. You may want to try a few tool suites to see which is the best fit for your experiment, goals, and desired outputs.
Several tutorials covering RNA-seq analysis in Galaxy are here: https://galaxyproject.org/learn/
General help for inputs and common usage questions can be found here: https://galaxyproject.org/support/
Not all tools are covered in tutorials but the general usage in Galaxy is the same as it would be line-command. Meaning, set the same options on the tool form as you would set options in the command string. The original tool manuals plus the help on the Galaxy tool forms will guide. But please let us know if you have trouble using a specific wrapped tool and we can help.
Thanks! Jen, Galaxy team