Difference between revisions of "Intro to RNA-Seq Data Analysis Course"
| Line 18: | Line 18: | ||
==Configuring PuTTY for connection == | ==Configuring PuTTY for connection == | ||
| − | * Server: marvin.st-andrews.ac.uk | + | * Server: <code>marvin.st-andrews.ac.uk</code> |
* Terminal | keyboard | check VT100+ | * Terminal | keyboard | check VT100+ | ||
* Window | Selection | Control use of Mouse | set xterm | * Window | Selection | Control use of Mouse | set xterm | ||
| Line 38: | Line 38: | ||
:- 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: | * For these two aspects, we have: | ||
| − | * A queue system to use, we shall request an interactive session ('''qrsh''') from the queue. | + | * A queue system to use, we shall request an interactive session ('''<code>qrsh</code>''') from the queue. |
* 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. | ||
| Line 47: | Line 47: | ||
screen | screen | ||
* This will open with quite bare screen except with a bottom line | * This will open with quite bare screen except with a bottom line | ||
| − | * | + | * There will be two command-line windows open. |
| − | * Two switch back and forth, you use Ctrl+l,n (n for next) or Ctrl+l,p (p for previous) | + | * Screen works on the activator key concept, you need ot use <code>Ctrl+l</code> 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. | ||
| + | * 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 13:11, 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 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+lto 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)
