Difference between revisions of "Intro to RNA-Seq Data Analysis Course"

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= Computing resources =
 
= Computing resources =
  
−
* RNA-Seq is a heavy workload, we need to be prepared for long-running tasks. This has two implications
+
* RNA-Seq is characterised by;
 +
:- heavy workload
 +
:- several software programs
 +
:- long-running tasks.
 +
 
 +
These have three implications:
 
:- The marvin cluster is an 11-machine '''shared''' computing resource, not a personal computer ... others are using it.
 
:- The marvin cluster is an 11-machine '''shared''' computing resource, not a personal computer ... others are using it.
 +
:- We need to load the special software before using it
 
:- We want to be able to have a process run unattended.
 
:- 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 ('''<code>qrsh</code>''') from the queue.
+
* For these three aspects, we have:
−
* We shall use the '''GNU Screen''' utility so we can do other things while waiting.
+
:- A queue system to use, we shall request an interactive session ('''<code>qrsh</code>''') from the queue.
 +
:- Use the ''module'' system to load, list and unload software programs
 +
:- We shall use the '''GNU Screen''' utility so we can do other things while waiting.
  
 
==GNU Screen ==
 
==GNU Screen ==
Line 46: Line 54:
 
To enter a new session:
 
To enter a new session:
 
  screen
 
  screen
−
* This will open with quite bare screen except with a bottom line
+
* This will open with quite a bare screen except with a bottom line.
 
* There will be two command-line windows open.
 
* There will be two command-line windows open.
 
* Screen works on the ''activator'' key concept, you need to use <code>Ctrl+l</code> (while <code>Ctrl</code>-key iis held down briefly, <code>l</code>-key is pressed) to activate any of its functions.
 
* Screen works on the ''activator'' key concept, you need to use <code>Ctrl+l</code> (while <code>Ctrl</code>-key iis held down briefly, <code>l</code>-key is pressed) to activate any of its functions.
 
* After pressing <code>Ctrl+l</code> and releasing you then have a series of single key strokes that will do various useful things.
 
* After pressing <code>Ctrl+l</code> and releasing you then have a series of single key strokes that will do various useful things.
 
* Two switch back and forth, you use <code>Ctrl+l,n</code> ('''n''' for next) or <code>Ctrl+l,p</code> ('''p''' for previous)
 
* Two switch back and forth, you use <code>Ctrl+l,n</code> ('''n''' for next) or <code>Ctrl+l,p</code> ('''p''' for previous)

Revision as of 14:13, 7 May 2017

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 characterised by;
- heavy workload
- several software programs
- long-running tasks.

These have three implications:

- The marvin cluster is an 11-machine shared computing resource, not a personal computer ... others are using it.
- We need to load the special software before using it
- We want to be able to have a process run unattended.
  • For these three aspects, we have:
- A queue system to use, we shall request an interactive session (qrsh) from the queue.
- Use the module system to load, list and unload software programs
- 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 a bare screen except with a bottom line.
  • There will be two command-line windows open.
  • Screen works on the activator key concept, you need to use Ctrl+l (while Ctrl-key iis held down briefly, l-key is pressed) 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)
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