Lesson motivation and learning objectives
Many researchers making the transition into genomics research (whether from another field or as their first research project) have not had prior experience with command-line tools. They may quickly run into situations in which they need to use command-line tools either because there is no good alternative for the type of anaysis they want to do or because they have so many data files that doing things manually on individual files is unfeasible.
This lesson will introduce learners to fundamental skills needed for working with their computers through a command-line interface (using the bash shell). They will learn how to navigate their file system, computationally manipulate their files (e.g. copying, moving, renaming), search files, redirect output and write shell scripts. By the end of the lesson, learners will be prepared to move on to using more advanced bioinformatic command line tools (see the lesson on Data Wrangling and Processing).
Lesson design
This lesson is meant to be taught in its entirety. For novice learners, schedule around 4 hours for this lesson. If your learners are already somewhat familiar with the bash shell, the earlier episodes can be condensed.