Principles and Applications of Modern DNA Sequencing


Session 1: Introduction to computational genomics

Today's topics:

Genome Structure

A Brief History of Genomics

An introduction to Codio

A quick introduction to the command line

Lines starting with hash (#) are only comments

    # This is the general format of unix command line tools
    $ program -option1 -option2 target

    # e.g., the 'pwd' program with no option or target
    $ pwd

I'll use a grey background to show the returned value


Hierarchical File System

Always know where you are and where your files are.

    # use the 'pwd' program with no option or target to ask where am I now?
    $ pwd

    # 'ls' shows the files and folders in a location (-l shows as a list)
    $ ls -l

    # the default target is here, but ls can be given a different target
    $ ls -l folder/

    # 'cd' moves you to a new location. Now 'pwd' will say you are there.
    $ cd folder/

Your location (current directory) starts from / (the root) and is described by a nested set of directory names leading to your location.

    # use 'pwd' program with no option or target to ask where am I now?
    $ pwd

We can make new directories and change our location.

    # make a new directory
    $ mkdir genomics

    # change directory (move) into the new directory and run pwd again
    $ cd genomics
    $ pwd

Learning bash command line tools

There are many great tutorials, and google always has an answer. If you have no background in using the terminal then you should complete the Linux Command Line Tutorial on Codio, listed under the Courses tab on the left.