The purpose of this short course is to teach researchers how to use the Linux operating system, thereby enhancing their ability to utilize various types of bioinformatics tools and support their research efforts.
Four workshops (total 10 hours)
Slatyer Room (Rm N2011) - Robertson Building #46
- Tuesday, 28 Feb 1.30-4.00pm
- Tuesday, 7 Mar 1.30-4.00pm
- Tuesday, 14 Mar 1.30-4.00pm
- Tuesday, 21 Mar 1.30-4.00pm
For each workshop, the class schedule is:
- 1.30-2.20pm (50min) Teaching
- 2.20-2.30pm (10min) Break
- 2.30-3.20pm (50min) Teaching
- 3.20-3.30pm (10min) Break
- 3.30-4.00pm (30min) Teaching
This course is also available online via Zoom.
- Connecting to a remote server
- Navigating through directories
- Creating and editing files
- Viewing file contents
- Moving, copying, deleting, and renaming files and directories
- Getting help with a command
- Linux file paths and structures
- Using shortcuts in Linux
- Using tmux to keep running your sessions in the background
- Piping and redirecting standard input and output
- Counting, sorting, and shuffling texts and file contents
- Finding and replacing texts
- Downloading and transfering data
- Using loops and statements
- Set up conda environment
- Assessing read quality using FastQC
- Quality control
- Trimming and filtering using trimmomatic
- Aligning reads to reference genome using BWA
- Variant calling using bcftools
- Writing a bash script about the workflow
- Using slurm to run jobs on the server
- Writing a sbatch file
- Parallel processing
Any enquiries please contact Jiajia Li at [email protected]