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Applied Bioinformatics Core |
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Here, you can find (some) of the code that we used during class.
The first two days are mostly bash commands covering raw reads and alignment.
Day 3 and 4 are based on Rmarkdown files.
None of these file may be completely fool proof since I have not tested them extensively, but they should give you a good idea of what we did during class.
The full 80+pages course notes can be found on our server or on zenodo.
Before there was MultiQC, you had to do your QC output wrangling yourself. This repo for previous class versions contains additional scripts that show you how some of the images (e.g., the bar charts of read alignment percentages) within the report were produced.