BME 383J Course Content

1. Log in to Lonestar via ssh
2. Copy data files that will be required for Thursday's homework:
   1. Define a BASH variable to the genomics data repository at TACC like this:
      How to define the variable BI in a bash shell

      BI="/corral-repl/utexas/BioITeam"
      

• Find $BI/ngs_course/intro_to_mapping/data
• Copy the three data files you find there to your scratch directory (see the Lonestar user's guide if you need help to get to your scratch directory).
• Figure out how to load the modules for samtools and bwa. Lonestar user guide helps here too.
• Bonus #1 - extract the genome from the gbk file and then map the fastq files to that genome. Help can be found elsewhere on this wiki site.
• Bonus #2 - do the human data scavenger hunt at the bottom of this wiki page (can be done on any computer - doesn't need TACC) to see what NGS data looks like.

Go to this web page and call variants from real human genomes from the 1000 genomes project.
Helpful hint: start this early - it involves some long run times at TACC.
IMPORTANT NOTE: you must use "-a BME2012" with the launcher_creator.py command.