Terminal, Unix & Files
UZH BIO392 HS22 - Day 03
Izaskun Mallona (email: izaskun.mallona at mls.uzh.ch).
Morning (on site, 9 am)
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 (on site or online)
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
- 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)
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.
For extra/advanced reading, please check the following tutorials on bash and awk: