Terminal, Unix & Files

UZH BIO392 HS23 - Day 03

Izaskun Mallona (email: izaskun.mallona at mls.uzh.ch).

Morning (on site)

We will have two lectures and several sets of exercises (on site).

• Unix + genomic formats lectures (exercises 1-4)
• Unix and genomic formats exercises (5-14)

Afternoon

We will run the SIB Unix course using a Web browser. We encourage you to run the exercises of the course in a terminal of your own; either on a GNU/Linux or MacOS; or with a Web browser-based emulator of your choice, like cocalc.

• SIB Unix course: UNIX for Bioinformatics
• Chapter 1: What is UNIX
• Chapter 2: The UNIX filesystem
• Chapter 3: UNIX shell - first steps
• Chapter 4: UNIX shell - filesystem commands
• Chapter 5: UNIX shell - working with files

Slides

• Genomic formats slides
• Project slides

UNIX training

Resources

• Exercises. Exercises 1-4 cover the basic usage of the terminal (morning). The full set of commands can be found at the SIB Course on UNIX.
• SIB Course on UNIX (afternoon)

File formats

Exercises

Exercises provide a flow of learning by doing.

• Exercises. Exercises 5-14 cover FASTA and FASTQ.

You can launch a terminal in MacOS and GNU/Linux. If running another OS, plese make use a a Web-browser based emulator or a Linux virtual machine.

Cheatsheets:

• Shell
• awk

For extra/advanced reading, please check the following tutorials on bash and awk:

• Shell
• awk