Difference between revisions of "Intro to RNA-Seq Data Analysis Course"
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* 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) | ||
| + | |||
| + | = Nature of the practicals = | ||
| + | * 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 17:10, 7 May 2017
Contents
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(whileCtrl-key iis held down briefly,l-key is pressed) to activate any of its functions. - After pressing
Ctrl+land 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) orCtrl+l,p(p for previous)
Nature of the practicals
- 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.
