Difference between revisions of "Intro to RNA-Seq Data Analysis Course"
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= Course schedule = | = Course schedule = | ||
| − | * This is a | + | * 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. | * Maximise practical aspect. | ||
* Having said that, if you fall behind, listening is better than catching up | * Having said that, if you fall behind, listening is better than catching up | ||
| − | Course website: <code>http://stab.st-andrews.ac.uk/ | + | Course website: <code>http://stab.st-andrews.ac.uk/i2rda/</code> |
= Connecting to a remote Machine = | = Connecting to a remote Machine = | ||
| Line 26: | Line 25: | ||
* Back to PuTTY main screen | select Default setting |click save | * Back to PuTTY main screen | select Default setting |click save | ||
| − | 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. | ||
| − | = | + | = Overview of RNA-Seq = |
| − | * | + | * For gene expression analyses, seen as a more powerful replacememnt to microarrays |
| − | |||
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| − | = | + | = 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. | |
| − | + | * Two switch back and forth, you use Ctrl+l,n (n for next) or Ctrl+l,p (p for previous) | |
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Revision as of 13:07, 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.
- Two switch back and forth, you use Ctrl+l,n (n for next) or Ctrl+l,p (p for previous)
