Today we are going to:

1. Refresh some shell commands, and maybe learning new ones
2. Start using bioinformatics programs, in addition to the standard Linux commands
3. Meet Perl for the first time. Nice to meet you!

Read this page (to the end) before starting the practical.

Before starting we now have an automatic script to check your presence. Type this command before starting:

appello Nome Cognome

You don’t need to use quotes.

 99% of the problems you report when using the Bash can be solved checking the files you are using (use the TAB!) and reading the error message. 

1. Bash and its commands

This time we expect from you to be accurate. During your first lab you messed around a little bit, meaning that files were not saved as expected. Remember that you are going to be evaluated also during the computer rooms practical.
The goal of this section is to make you mastering the terminal, so go and destroy!

This part is mandatory, but starting taking an online quiz .

Open the “Bash (part2)” page

2. First bioinformatics programs

As we said before commands are actual programs, and typing “ls” is actually making a program – called `ls`, starting up. What makes commands so special is that they are widespread and installing a UNIX like operating system means that most of them are available by default. Today we will perform two tasks using existing programs:

1. Simulate a “whole genome shotgun” of the E. coli genome you downloaded
2. Align the reads produced by the simulation against the reference

We installed some programs in /home/geno/bin/. This is an absolute path, and note that if you are in your home folder the relative path is ../bin/.

Open the “first programs” page

3. Meet Perl

Ready to start playing with a programming language? Go there then!
This part is optional and you can do it at home as well (no Linux needed)

Open the “first time with perl” page

BEFORE LEAVING
Please, don’t forget to refresh this page to check updates and before leaving:

• Type the goodbye command
• Log out from the PC
• Put the chair under the desk