Analytics 2: Introduction to the command-line for Bioinformatics
Module Coordinator Mark Dunning
Course Content
This course offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We give example of processing data arising from Next-Generation Sequencing experiments, in particular an RNA-seq experiment.
Pre-requisites
No prior programming experience is required. Computers will be provided. You can bring your own laptop to the workshop if you wish but it will need a working wi-fi connection and you will have to let the tutor know in advance so a temporary York password can be created for you.
Learning Outcomes
After this course you should be able to:
- Connect to a Unix / Linux system
- Navigate around a file system by issuing commands; rather than using a Desktop environment
- Move and copy files and directories within the Linux system
- Work with text files
- Run programs from the command-line
- Run quality assessment tools on data derived from High-throughput sequencing experiments
- Write short scripts to document an analysis
Schedule (Provisional)
- 10:00 - 10:30 Course Setup
- 10:30 - 12:45 Introduction to the command line
- 13:30 - 14:30 Obtaining sequencing data and assessing quality
- 14:30 - 16:00 Aligning sequencing data and quantification
Unix “cheatsheet”
Course Feedback
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