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_2016/day_1_partA . #for this specific exercise cd day_1_partA/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.
First you need all the files. One is missing. Download it from here -> genes.1 and transfer it to your lonestar5 account (under day_1_partA/tacc_exercise)
Make a commands file with the unix commands to print the first 10 lines of each file into an output file.
Use launcher_creator.py to create a launcher to submit this job (command file).
Submit the job.
Use our summer school reservation when submitting jobs to get higher priority:
sbatch --reservation=intro_NGS
Check the queue.
Check the output files and log files.
BACK TO COURSE OUTLINE