Feeling overwhelmed by it all? You're not in this alone! Rea d this SEQanswers post about biologists starting to analyze NGS data : http://seqanswers.com/forums/showthread.php?t=4589
That post mentions a great resource for biologists beginning to work in the Unix enviornment: the Unix and Perl for Biologists website. These kind folks have put together a tutorial that you can work (with some modifications) on TACC. This page shows you how to do just that.
First, login to TACC:
ssh <userid>@lonestar.tacc.utexas.edu
In your home directory, create a directory for the tutorial. This name "Volume/USB" is an attempt to match the pathnames in the tutorial as much as possible.
mkdir -p Volume/USB
Prepare the tutorial resources in this directory:
cd Volume/USB cp /corral-repl/utexas/BioITeam/downloads/unix_and_perl_v3.0.zip . unzip unix_and_perl_v3.0.zip
This creates a directory Unix_and_Perl_course that contains the tutorial files.
It is important to note that this tutorial was designed to run on an Apple Mac, so some things in it will not be quite the same on TACC. In fact, in order for things to work at all, you must replace names in the tutorial that start with /Volume/USB with ~/Volume/USB.
Before you start the tutorial, it might help to have this Cheat sheet of useful Unix commands open in a browser window.
Now you're ready to dive in. Open the Unix and Perl primer for biologists and start on p 15