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Due to the size of the data and length of run time, most of the programs have already been run for this exercise. The commands run are in the directory run_commands. We will spend some time looking through these commands to understand them. You will then be parsing the output, finding answers, and visualizing results (in the directory results).
resolve insert size? resolve strand inf
Run tophat
On lonestar, to run tophat, following modules need to be loaded.
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