Pre-course Material

1. Make sure you can connect to uppmax using a terminal. If you use a pc we recommend MobaXterm (http://mobaxterm.mobatek.net)
2. If you still feel uncertain how to work in a terminal please take time to do the first three parts in the “Unix tutorial for beginners” that can be found here http://www.ee.surrey.ac.uk/Teaching/Unix/ before the course starts. Otherwise you will not be able to take in the practical parts.
3. Make sure that you can read and write in the course folder by creating a file or folder in the /proj/g2015054/completed folder. Download IGV on your own computer and make sure that you have hg19 genome available. The data we will work with is from human and we will visualise the results in the IGV genome browser. IGV can be downloaded from the broad institute (https://www.broadinstitute.org/igv/).
4. Install R on your own computer (the latest version).
5. Install Rstudio on your own computer to run all your commands (This is optional). Rstudio is a very powerful GUI for structuring your R code in a good way.
6. In R install the latest version of DEseq2 (This is optional). We will work with this program during the course and it takes a while to install so if you can do it before you will not have to waste time installing during the exercise time. More instructions how to install the package can be found here https://bioconductor.org/packages/release/bioc/html/DESeq2.html