Welcome to the 2013 TGAC biology workshop

3. Titus Brown <ctb@msu.edu> and Alexandra Pawlik <a.pawlik@software.ac.uk>

We will use this Etherpad site to distribute commands.

Explain: minute cards; stick notes on monitors.

• Session 1: command line & BLAST
  • Welcome!
  • BLAST
• Session 2: mRNAseq assembly and annotation
  • Copying common files around
  • Working with mRNAseq data
• Session 3: Shell and shell scripting
  • What is the shell and how do I access the shell?
  • Hello, World!
  • Moving around the file system
  • File Types
  • Changing Directories
  • Arguments (flags)
  • Examining the contents of other directories
  • Full vs. Relative Paths
  • Saving time with shortcuts, wild cards, and tab completion
  • Which program?
  • Examining Files
  • Redirection
  • Creating, moving, copying, and removing
  • Count the words
  • The awesome power of the Pipe
  • A sorting example
  • Searching files
  • Finding files
• Session 4: data analysis in IPython Notebook

Indices and tables

• Index
• Module Index
• Search Page