Table of contents


This exercise will be partially on the command line, and partially using Rstudio. For the command-line part of the exercise, please use a console window to connect to the AMI via ssh (if you’re on Mac or Linux), by typing ssh ubuntu@YOUR_PUBLIC_DNS . If you’re on Windows, please use PuTTy instead of ssh to connect to the AMI. When you run Rstudio, please do so in a browser window of your own machine, by specifying http://YOUR_PUBLIC_DNS:8787 as we did before for other exercises.

Once you’re connected to your AMI instance with ssh or PuTTY, you’ll need to execute a couple of commands in order to set up your instance for the SweeD exercise. These are given below, and copy-pasting should work fine.

cd ~/wpsg_2016/software/
mkdir sweed
cd sweed
tar -xzf SweeD_v3.2.1_Linux.tar.gz
cd SweeD_v3.2.1_Linux
cd ~/wpsg_2016/activities/
mkdir sweed
cd sweed
tar -x -f Jones.tar
tar -x -f BenLim.tar
tar -x -f sweed.input.tar

After this you should have 48 bam-files (and associated bai-files) in your current directory. Check if this is the case with
ll *.bam | wc -l


Please find an introduction to today’s exercise here.

Exercise 1

Please find instructions for exercise 1 here.

Exercise 2

Please find instructions for exercise 2 here.