In this section are some BAGA analyses that should be useful for learning workflows for typical analyses. They also demonstrate how BAGA can be useful for reproducible research because by pasting each command into a linux terminal, you should be able to reproduce the results on your own computer. Simple scripts can therefore be published to accompany your published work. Where possible (the majority of cases), required software is installed automatically and particular versions for each tool can be specified to give the best chances of reproducibility.