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

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= Course schedule =
 
= Course schedule =
  
−
* This is based on a 2 day Edinburgh Genomics course of the same name.
+
* This is based on a 2 day Edinburgh Genomics course of the same name, with the following changes:
−
* Intro to Linux, Sequencer visits and technology iparts taken out. Also, less theory.
+
:- "Introduction to Linux" moduel excluded
−
* Maximise practical aspect.
+
:- "Sequencer technology overview" module excluded.
−
* Having said that, if you fall behind, listening is better than catching up
+
:- No laboratory visit
 +
:- 50% of that course was theoretical, this will be reduced to 30%
  
−
Course website: <code>http://stab.st-andrews.ac.uk/i2rda/</code>
+
* Each section begins with a "Talk", and then a practical runthrough.
 +
* If necessary, some talk slides may be skipped, as the main idea is getting through the practicals.
 +
* Having said that if major theoretical points arise during a practical, they will be discussed.
 +
* Course website: <code>http://stab.st-andrews.ac.uk/i2rda/</code>
 +
:- this has all the presentations and practicals
  
 
= Connecting to a remote Machine =
 
= Connecting to a remote Machine =
Line 26: Line 31:
  
 
You should now be able to "open" a session
 
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.
+
* Be aware typing 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 =
 
= Computing resources =
Line 49: Line 50:
 
:- We shall use the '''GNU Screen''' utility so we can do other things while waiting.
 
:- We shall use the '''GNU Screen''' utility so we can do other things while waiting.
  
−
==GNU Screen ==
+
=GNU Screen 1 =
  
−
Simply allows several command-line sessions to which you switch back and forth.
+
A program which allows several command-line sessions open, similar to the idea of open tabs in a web browser. Let's try it out.
−
To enter a new session:
+
* To enter a new session, type <code>screen</code>
−
screen
+
* This will open with quite a bare screen except with a indicator line at the bottom.
−
* 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 <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)
+
* There will be two command-line windows open when you start it.
 +
* Let's learn how to get out of it first
 +
:- type <code>exit</code>, you should see you have one command-line session less.
 +
:- type <code>exit</code> again and you will be told you have exited screen
 +
:- you are now back in the ordinary command-line.
 +
 
 +
= GNU Screen 2 =
 +
* Go back into screen
 +
* Switch back and forth between the two open sessions: use <code>Ctrl+l,n</code> ('''n''' for next) or <code>Ctrl+l,p</code> ('''p''' for previous)
 +
* Don't see anything different when you do this? Look again at the bottom line, the asterisk has changed position.
 +
:- the asterisk define the active session
 +
: you can move to a numbered session with <code>ctrl+l,1</code> or <code>ctrl+l,2</code> for session no.1 and no.2 respectively.
 +
 
 +
= Overview of RNA-Seq =
  
−
= Nature of the practicals =
+
* For gene expression analyses, seen as a more powerful replacememnt to microarrays
−
* Each module is self-sufficient. You do not have to finish one to start another.
 
−
:- Unlike a real-world pipeline, each part has it previously prepared input files.
 
−
* The data has been modifed to suit the training course. It is less troublesome than raw real-world data because there isn't time to deal with artefact such as contamination.
 

Revision as of 11:23, 10 May 2017

Course schedule

  • This is based on a 2 day Edinburgh Genomics course of the same name, with the following changes:
- "Introduction to Linux" moduel excluded
- "Sequencer technology overview" module excluded.
- No laboratory visit
- 50% of that course was theoretical, this will be reduced to 30%
  • Each section begins with a "Talk", and then a practical runthrough.
  • If necessary, some talk slides may be skipped, as the main idea is getting through the practicals.
  • Having said that if major theoretical points arise during a practical, they will be discussed.
  • Course website: http://stab.st-andrews.ac.uk/i2rda/
- this has all the presentations and practicals

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 typing in your password is done blindly. I.e. it does not appear on the screen.

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 1

A program which allows several command-line sessions open, similar to the idea of open tabs in a web browser. Let's try it out.

  • To enter a new session, type screen
  • This will open with quite a bare screen except with a indicator line at the bottom.
  • 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.
  • There will be two command-line windows open when you start it.
  • Let's learn how to get out of it first
- type exit, you should see you have one command-line session less.
- type exit again and you will be told you have exited screen
- you are now back in the ordinary command-line.

GNU Screen 2

  • Go back into screen
  • Switch back and forth between the two open sessions: use Ctrl+l,n (n for next) or Ctrl+l,p (p for previous)
  • Don't see anything different when you do this? Look again at the bottom line, the asterisk has changed position.
- the asterisk define the active session
you can move to a numbered session with ctrl+l,1 or ctrl+l,2 for session no.1 and no.2 respectively.

Overview of RNA-Seq

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