Intro to RNA-Seq Data Analysis Course - Revision history

Rf at 16:21, 11 May 2017

2017-05-11T16:21:56Z

Rf at 16:11, 11 May 2017

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Rf at 16:00, 11 May 2017

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Rf at 15:14, 11 May 2017

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Rf at 14:10, 11 May 2017

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Rf at 10:26, 10 May 2017

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Rf at 10:23, 10 May 2017

2017-05-10T10:23:47Z

Rf at 17:10, 7 May 2017

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@@ Line 106: / Line 106: @@
 = Recovering a session =
-* Now detach a session, it will stay running, and then go back to it
+* Now detach a session, <code>ctrl+l,d</code> to detach
-:- <code>ctrl+l,d</code> to detach
+* Now you're outside screen, you can log out, switch off and go home if you like (don't please).
-* Now you're outside screen, you can log out.switch off and go home if you like (don't please)
+* Next type <code>screen -r</code> to re-attach.
 :- did the process stop?
 :- unfortunately this cannot be done with many graphical programs
 :- though some have a command-line mode, where it is possible
 * Type ctrl+c, to stop it, demonstration over.

@@ Line 58: / Line 58: @@
 = Aspects of using Windows terminals to connect to Linux =
-* You can run the Windows web-browser (Chrome preferred) and copy text selecting and <code>ctrl+c</code>
+* You can pen the <code>http://st-andrews.ac.uk/i2rda</code> site on the Windows web-browser (Chrome preferred) and copy text selecting and <code>ctrl+c</code>
-* This can then be pasted inside the putty command-line by clicking the middle mouse button.
+* This can then be pasted inside the PuTTY command-line by clicking the middle mouse button.
 * In many ways, copy-pasting is not great for learning.
 :- although some of the commands are too long to type out, even with history and tab-completion.
@@ Line 103: / Line 103: @@
 * let's get something trivial running here: execute the <code>prtgn.sh</code> script by typing <code>prtgn.sh</code>, then <code>RETURN</code>, and let it print out gene names to its heart's content.
 :- it's not drosophila, so only some of them are funny.
 * Now detach a session, it will stay running, and then go back to it
 :- <code>ctrl+l,d</code> to detach
@@ Line 110: / Line 113: @@
 :- unfortunately this cannot be done with many graphical programs
 :- though some have a command-line mode, where it is possible

@@ Line 92: / Line 92: @@
 :- the asterisk defines the active session
 :- you can move to a numbered session directly with <code>ctrl+l,1</code> or <code>ctrl+0,1,2</code> for sessions 0, 1 and 2.
 = Getting a Queue slot =
@@ Line 102: / Line 99: @@
 * Type <code>qrsh</code> which requests a queue slot ... it will take a little time to give you one.
 :- we shall not use this slot for the graphical programs, only the processing ones.
-:-
+* When you get a slot, notice if you are still on marvin, or one of the nodes (assignment is based on load usually)

@@ Line 35: / Line 35: @@
 Note: If you don't have your password, please ask to have it reset for you.
-= Computing resources =
+= Computing resources notes =
 * RNA-Seq like other Next Generation Sequencing technologies, is characterised by;
@@ Line 52: / Line 52: @@
 :- We shall use the '''GNU Screen''' utility so we can do other things while waiting.
-= Aspect of using Windows terminals to connect to Linux =
+= Computing resources diagram =
 [[File:marv.png]]
 * You can run the Windows web-browser (Chrome preferred) and copy text selecting and <code>ctrl+c</code>
@@ Line 61: / Line 64: @@
 :- try to also use tab-completion, and the history (<code>up</code>/<code>down</code> arrows and <code>Ctrl+r</code>)
-Weakness to watch out for:
+<ins>Weakness to watch out for</ins>:
 * The marvin cluster (more precisely, the network it's attached to) doesn't carry graphics so well.
 * We shall be using several graphical programs, and they are all likely to run slowly.
@@ Line 74: / Line 77: @@
 * <code>screen</code> 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.
-* There will be two command-line windows open when you start it.
+* There will be one command-line session open when you start it.
 * Let's learn how to get out of it first
 :- type <code>exit</code> again and you will be told you have exited <code>screen</code>.
 :- you are now back in the ordinary command-line.
 = GNU Screen 2 =
-* Go back into screen
+* Go back into screen, type <code>screen</code>.
-* 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)
+* you open a new session with <code>ctrl+l,c</code> which '''c'''reates a new session.
 * Don't see anything different when you do this? Look again at the bottom line, the asterisk has changed position.
 :- the asterisk defines 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.
+:- you can move to a numbered session directly with <code>ctrl+l,1</code> or <code>ctrl+0,1,2</code> for sessions 0, 1 and 2.
-:- you open a new session with <code>ctrl+l,c</code> which '''c'''reates a new session.
+* you can detech a session, it will stay running, and then go back to it
 = Getting a Queue slot =
@@ Line 94: / Line 102: @@
 * Type <code>qrsh</code> which requests a queue slot ... it will take a little time to give you one.
 :- we shall not use this slot for the graphical programs, only the processing ones.
 :-

@@ Line 53: / Line 53: @@
 = Aspect of using Windows terminals to connect to Linux =
-[[File:marvv.png]]
+[[File:marv.png]]
 * You can run the Windows web-browser (Chrome preferred) and copy text selecting and <code>ctrl+c</code>

@@ Line 31: / Line 31: @@
 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.
+* 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;
+* RNA-Seq like other Next Generation Sequencing technologies, is characterised by;
-:- heavy workload
+:- heavy computational workloads
-:- several software programs
+:- many different software programs, sometimes doing the same thing, which can be arranged into a pipeline.
 :- long-running tasks.
@@ Line 49: / Line 51: @@
 :- 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 =
@@ Line 70: / Line 86: @@
 :- 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.
 :- you open a new session with <code>ctrl+l,c</code> which '''c'''reates a new session.
 = Overview of RNA-Seq =
 * For gene expression analyses, seen as a more powerful replacememnt to microarrays

@@ Line 1: / Line 1: @@
 = 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
-Course website: <code>http://stab.st-andrews.ac.uk/i2rda/</code>
+* Each section begins with a "Talk", and then a practical runthrough.
 = Connecting to a remote Machine =
@@ Line 26: / Line 31: @@
 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.
 = Computing resources =
@@ Line 49: / Line 50: @@
 :- 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.
 * 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.
-* 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.
-= Nature of the practicals =
+* For gene expression analyses, seen as a more powerful replacememnt to microarrays

← Older revision		Revision as of 17:10, 7 May 2017
Line 59:		Line 59:
	* 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.