Next-Generation Sequencing

Palais de Congres, Montreal, Quebec
Apr 14, 2014
9:00 am - 4:30 pm

Presentation

The presentation slides are available -- PPTX and PDF.

Tutorial instructions

  1. Find your machine name at this link and save it in a notepad.
  2. Download amazon.pem and save it to your computer as a .PEM file.
  3. Log in: Windows instructions or Mac OS X instructions. Use username 'ubuntu', not 'root'; pull machine names from here.
  4. Execute sudo bash to change to the super-user account once you're logged in.
  5. The first time only,
    mkdir /mnt/data
    ln -fs /mnt/data /data
    cd /data
    curl -O http://public.ged.msu.edu.s3.amazonaws.com/mrnaseq-subset.tar
    tar xvf mrnaseq-subset.tar
    
  6. Optionally, install dropbox.
  7. For mRNAseq, start at the Eel Pond protocol Note: if you want to start at the diginorm stage (#2), you can type:
    cd /mnt/work
    curl -O http://public.ged.msu.edu.s3.amazonaws.com/mrnaseq-extract-qc.tar
    tar xf mrnaseq-extract-qc.tar
    
  8. Later in the day, we may do the variant calling tutorial.

Running things on your own Ubuntu 12.04 machine

Follow the apt-get instructions here to install the necessary components to run these tutorials on your own. You'll need to start with a blank Ubuntu 12.04 machine.

Other links to look at: