Intro to RNA-Seq Data Analysis Course

Course schedule

• This is based on a 2 day Edinburgh Genomics course of the same name.
• Intro to Linux, Sequencer visits and technology iparts taken out. Also, less theory.
• Maximise practical aspect.
• Having said that, if you fall behind, listening is better than catching up

Course website: http://stab.st-andrews.ac.uk/i2rda/

Connecting to a remote Machine

Presenting this before introduction as some people might experience delays logging in.

• We shall use a remote machine not the machine you are logged into locally
• The program we shall use is PuTTY.
• Please try to locate PuTTY in the applications section or on AppsAnywhere

Configuring PuTTY for connection

• Server: marvin.st-andrews.ac.uk
• Terminal | keyboard | check VT100+
• Window | Selection | Control use of Mouse | set xterm
• Connect | Data | enter username
• Connection | ssh | X11 Forwarding | Check yes
• Back to PuTTY main screen | select Default setting |click save

You should now be able to "open" a session

• Be aware typng in your password is done blindly. I.e. it does not appear on the screen.

Overview of RNA-Seq

• For gene expression analyses, seen as a more powerful replacememnt to microarrays

Computing resources

• RNA-Seq is a heavy workload, we need to be prepared for long-running tasks. This has two implications

- The marvin cluster is an 11-machine shared computing resource, not a personal computer ... others are using it.

- We want to be able to have a process run unattended.

• For these two aspects, we have:
• A queue system to use, we shall request an interactive session (qrsh) from the queue.
• We shall use the GNU Screen utility so we can do other things while waiting.

GNU Screen

Simply allows several command-line sessions to which you switch back and forth. To enter a new session:

screen

• This will open with quite bare screen except with a bottom line
• There will be two command-line windows open.
• Screen works on the activator key concept, you need ot use Ctrl+l to activate any of its functions
• After pressing Ctrl+l and releasing you then have a series of single key strokes that will do various useful things.
• Two switch back and forth, you use Ctrl+l,n (n for next) or Ctrl+l,p (p for previous)