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Welcome to the 2013 TGAC biology workshop¶

  1. 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

Table Of Contents

  • Welcome to the 2013 TGAC biology workshop
  • Indices and tables

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