Pre-course Material

  1. If you do not already have an Uppmax account, create an Uppmax account following these instructions.

  2. Log in to SUPR and request membership in the project g2018025.

  3. Make sure you can connect to Rackham at Uppmax using a terminal. If you use a pc we recommend MobaXterm (http://mobaxterm.mobatek.net) or Windows 10 Bash for Linux.

  4. 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 workshop starts. Otherwise you will not be able to take in the practical parts.

  5. Make sure that you can read and write in the workshop folder by creating a file or folder in the /proj/g2018025/completed folder. If you cannot write to the folder, the most likely reason is that you have not requested acess to the workshop project via SUPR. OBS! It may take an hour or so from the time your access is approved before you can actually write to the folder.
    We will check before the workshop that all students have logged in and done this, so do not forget!

  6. 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/).

  7. Install R on your own computer (the latest version), instructions can be found here.

  8. 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.

  9. If you feel that you need to touch up on your R-skills before the course start, we recommend that you go through some basic tutorials before the course starts. A list of useful tutorials can be found here.

  10. In R, install the latest version of DEseq2 (This is optional). We will work with this program during the workshop 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.