This repository will contain the approximate schedule and the list of notes and materials for the informal bioinformatics workshop taught by Piotr Łukasik at the Institute of Environmental Sciences. This is very much work in progress --- but hopefully, will help you stay on top of things!
- Introduction: Who is attending? What the workshop is about?
- Why command line?
- What is Linux? How to get started?
- Basic Linux commands: finding your way in the Linux environment.
- Files, directories/folders and paths
- Homework :)
- Working on the cluster: logging in, copying files. htop.
- Brief recap of basic commands: pwd / ls / cd / mkdir / touch / cp / mv / rm
- Folder and file permissions. chmod.
- Displaying file contents: less, nano. cat. Top and bottom lines: head, tail.
- Redirecting output
- Getting basic stats: wc
- Searching text files - grep
- Pipes
- Practical examples and exercises
- moving files to/from the cluster
- modifying text - sed
- cut, sort, uniq
- finding programs. $PATH. .bashrc.
- loops
- What are regular expressions? Why and how to use them?
- Basic syntax
- More advanced syntax :)
- Practical examples and exercises
- Using REGEX with grep in the command line
- Using REGEX with sed in the command line
- Exercises :)
- Homework
- Screen
- $PATH and .bashrc
- conda
- What programming is about? Why program? What are the main categories of programming languages? What are the main concepts and terms?
- Variables - types. Arrays - types. How they work in the Python environment?
- What are loops and IF statements? How to use them in the Python environment?
- What are the key components of a simple Python script?
- How to use variables and arrays in real life?
- Reviewing homework. How to make your scripts more efficient?
- Methods to be applied on variables
- Input and Output files
- Editing sequence files - how to organize the workflow?