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bash-beginners-2018 [2020/02/07 09:51] (current)
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 +====== Bash for beginners ======
 +===== General information =====
 +=== Who is this course for ===
 +This course is for biologists aiming to learn how to use the **Linux Command Line** to perform bioinformatics analyses. It requires no prior knowledge of the command line.
 +=== Avoid this course if... ===
 +If you are already able to use basic shell commands, and in particular to tell programs //where your file are//, you probably don't need this course.
 +=== How we will work ===
 +You'll have full access to a **Linux Server**, so the course heavily relies on this website to provide you workshop notes to follow at your pace from your office (or living room :-D ). Each lesson introduce the concepts and let us review the problems found during the previous session and to begin working on the new assignment. You'll have 24/7 access to the remote Linux server, so the time we spend together is mainly to introduce concepts and to discuss problems, while the real "​tutorial"​ can be self paced and done during the week when you have some spare time.
 +The course spans across **three weeks**, the the first with two lessons, then one lesson for the last two. 
 +Bring your laptop (any model will work). The course will be fully accessible also from non-NBI laptops.
 +=== A small "​preview"​ ===
 +Watch a [[https://​vimeo.com/​257159096|short video]] describing the content of the course.
 +===== Signup =====
 +Please fill this [[https://​docs.google.com/​forms/​d/​e/​1FAIpQLSdf6ZAVWqpGpKNpcH3cbJ56gklP9_K5JpK0ipMUausqLzIS8A/​viewform|form]] to Sign Up!
 +===== Program =====
 +Each day we will meet in a room at QIB (details to be confirmed), from **9.30** to **12.00**. Bring your own laptop, if you need one contact Andrea in advance to arrange an alternative.
 +==== Day1: The first tour ====
 +**April 11th, Rollesby N215 Meeting Room**
 +A **[[bash-first|brief introduction]]** to the core concepts of the command line as a good environment for bioinformatics analysis. A hands-on tutorial to log in into a remote Linux server using each participants laptop, and test the first commands.
 +Our main goal is the set up of your clients, in order to allow you off-site access to the workshop!
 +    - What is a terminal: the "​terminal prompt"​
 +    - Accessing a remote server using ''​ssh''​ (Mac or Linux) or the program PuTTY (from Windows)
 +    - Using ''​screen''​ to set up a persistent session on a remote server
 +    - The filesystem: using ''​pwd''​ and ''​ls''​ to interact with it from the terminal. Tab completion.
 +    - ''​mkdir'' ​ to create directories
 +    - A command line text editor: ''​nano''​
 +==== Day 2: basic commands ====
 +**April 13th, Barton E301 Meeting Room** ​
 +**[[bash-second|Understanding the "file system"​]]**,​ relative and absolute paths, and the commands to organize the directories,​ to list files, to copy and move files and directories. Introduction to commands to interact with text files and view them.
 +We will use the **FASTA** and **FASTQ** file formats as examples.
 +    - ''​ls''​ (with some parameters),​ wildcards, ''​cd'',​ ''​rmdir'',​ ''​find''​
 +    - Interactive visualization of text files: ''​less''​
 +    - Viewing text files with ''​cat'',​ ''​head''​ and ''​tail''​
 +    - Counting lines and characters with ''​wc''​
 +    - Selecting lines with patterns using ''​grep'' ​
 +    - Redirecting a command output into a text file
 +==== Day 3: Extracting data from text files ====
 +**April 20th, Rollesby N215 Meeting Room**
 +Using terminal commands to **[[bash-3|interact with bioinformatics files]]**. We'll introduce the SAM file format used to store NGS mapping, the VCF format (for SNP calling), and some tabular annotation files (**GFF**, **GTF**).
 +    - Recap of previous commands to be used with for SAM files 
 +    - Downloading datasets with ''​wget''​
 +    - The ''​sort'',​ ''​uniq'',​ ''​cut''​ commands
 +    - Command pipes: combining multiple commands
 +====  Day 4: The bioinformatician'​s perspective ====
 +**May 2nd, Rollesby N215 Meeting Room**
 +Using **[[bash-4|short reads alignment]]** as a theme, we'll introduce how to install new software to be used from the command line, users and file permissions,​ and of course the alignment program **bwa** and **samtools** the swiss army knife to manipulate SAM files.
 +    - Using ''​bwa''​ to align short reads
 +    - Using ''​samtools''​ to operate with SAM/BAM files