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Get your data

Get set up
cds
mkdir my_rnaseq_course #this is where you'll be doing all the course exercises
cd my_rnaseq_course
 
cp -r /corral-repl/utexas/BioITeam/rnaseq_course/tacc_exercise .  #for this specific exercise
cd tacc_exercise

Exercise:

Run a simple command on each of these four files. We are going to just print the first 10 lines of each file.

  1. Make a commands file with the unix commands.

     Hint

    Open an editor to create a file called commands

    Use head command to print the first 10 lines.

     Answer
    nano commands
    	head genes.1
    	head genes.2
    	head genes.3
    	head genes.4  #ctrl+x to exit
  2. Use launcher_creator.py to create a launcher to submit this job (command file).

     Hint

    launcher_creator.py -h to see the options.

     Answer
    launcher_creator.py -n exercise -t 01:00:00 -j commands -q development -a CCBB
  3. Submit the job.

     Hint

    qsub

     Answer
    qsub exercise.sge
  4. Check the queue.

     Answer

    qstat

  5. Check the output files and log files.

     Hint

    Look at <jobname>.o* file for output information

    Look at <jobname>.e* file for log/error information

     Answer
    less exercise.o* #q to exit
    less exercise.e* #q to exit

 

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