# RNA-Seq DGE Workflow

http://stackoverflow.com/questions/600079/is-there-any-way-to-clone-a-git-repositorys-sub-directory-only
http://stackoverflow.com/questions/160608/do-a-git-export-like-svn-export
git checkout-index -a -f --prefix=/destination/path/



## How to use it?

git checkout-index -a -f --prefix=/destination/path/

1) Optionally rename dge_master.sh to something like dge_mouse_helin.sh
2) Adjust paths in master script
3) Run on madmax
4) Adjust reports if necessary


## How to backport changes into it?

Clone it, change it, push and commit it.