tbooth
commented
11 months ago I disagree with this one. I think anyone who's not completed Shell Novice or similar is not ready for this course, as we throw around terms like "shell script" and "variables" and "output redirection" without pre-amble. Anyone who's never written a shell script (or similar) is probably not going to even get what Snakemake is doing for them.
I'll add a couple of links to where people can read up on FASTQ files and read mapping.
From @tkphd
The lesson homepage lists the following prerequisites:
Familiarity with the Bash command shell, including concepts like pipes, variables and loops. Knowledge of bioinformatics fundamentals like the FASTQ file format and short read mapping, in order to understand the example workflow. I suggest rephrasing to state the actual prerequisites, and separately enumerate background that would be helpful but is not strictly necessary.
Prerequisites:
Some background navigating the Unix filesystem and editing files through the command line, as taught in Shell Novice or similar. Optional background:
To help understand the shell-based workflow this lesson takes as its starting point, familiarity with Unix shell pipes, loops, and variables is encouraged. Some familiarity with FASTQ files and short read mapping will help learners who seek a deep understanding of the example workflow.