Changes

From Genome Analysis Wiki
Jump to navigationJump to search

SeqShop: Calling Your Own Genome, December 2014 (view source)

Revision as of 19:33, 9 December 2014

341 bytes removed ,  19:33, 9 December 2014
no edit summary
Line 102: Line 102:     
<div class="mw-collapsible" style="width:500px">
 
<div class="mw-collapsible" style="width:500px">
−
== Wednesday Checking if INDEL Completed ==
+
== Wednesday ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
=== Logging Back in to Check Jobs ===
+
 
 +
=== Checking if INDEL Completed ===
 +
==== Logging Back in to Check Jobs ====
    
;How do you log back into screen?
 
;How do you log back into screen?
Line 120: Line 122:  
</div>
 
</div>
   −
== Wednesday - Structural Variation Tutorial ==
+
=== Structural Variation Tutorial ===
 
Now we are going to run the Structural Variation Practical
 
Now we are going to run the Structural Variation Practical
   Line 128: Line 130:     
<div class="mw-collapsible" style="width:500px">
 
<div class="mw-collapsible" style="width:500px">
−
== Wednesday - Start SNP Calling ==
+
=== Start SNP Calling ===
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
=== Setup ===
+
==== Resume screen ====
−
The indel & snpcall pipelines will run overnight, but you'll want to log out.
  −
; How do I leave something running on the server even if I log out?
  −
: One solution is screen!
     −
; How do I use screen?
+
;How do you log back into screen?
−
: Before running your command, you need to start screen:
+
screen -r
−
: <pre>screen</pre>
+
This will resume an already running screen.
   −
[[File:Screen.png]]
+
Verify you got a "completed successfully" message.
   −
As it says, press <code>Space</code> or <code>Return</code>.
+
How long did INDEL calling take?  Look at the log message - time in seconds.
−
* It should now look basically the same as your normal command line.
     −
Set these values.  Also, be sure to specify your sample name instead of SampleXX
+
Detach from screen.  We will resume it again later when we start SNPCall.
−
export SAMPLE=SampleXX
+
  Ctrl-a d
−
  source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
     −
See the settings you just used:
+
Your screen session still has your environment variables set, so you do not need to reset them.
−
cat /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
  −
Shows you:
  −
:<code>export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud</code>
  −
:<code>export SS=/net/seqshop-server/home/mktrost/seqshop/singleSample</code>
  −
:<code>export OUT=~/$SAMPLE/output</code>
     −
=== List of BAMs ===
+
==== List of BAMs ====
 
The list of BAMs has already been created (just 1 BAM, your sample).
 
The list of BAMs has already been created (just 1 BAM, your sample).
 
* But it is simply SAMPLE\tBAM_name, so easy to figure out
 
* But it is simply SAMPLE\tBAM_name, so easy to figure out
Line 164: Line 156:  
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
 
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
   −
=== Configuring SnpCall ===
+
==== Configuring SnpCall ====
    
  cat ~/$SAMPLE/gotcloud.conf
 
  cat ~/$SAMPLE/gotcloud.conf
Line 192: Line 184:  
</pre>
 
</pre>
   −
==== Configuration Updates ====
+
===== Configuration Updates =====
 
In order to complete SnpCall overnight, we are going to tell GotCloud to only call SNPs for the EXOME regions.
 
In order to complete SnpCall overnight, we are going to tell GotCloud to only call SNPs for the EXOME regions.
   Line 203: Line 195:  
* See [http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline#Targeted.2FExome_Sequencing_Settings|Targeted/Exome Sequencing Settings] for more information on the GotCloud configuration settings for running Targeted/Exome runs.
 
* See [http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline#Targeted.2FExome_Sequencing_Settings|Targeted/Exome Sequencing Settings] for more information on the GotCloud configuration settings for running Targeted/Exome runs.
   −
=== Running SnpCall ===
+
==== Running SnpCall ====
 
Run GotCloud snpcall with 6 jobs running in parallel
 
Run GotCloud snpcall with 6 jobs running in parallel
 
* Why 6?   
 
* Why 6?   
Line 213: Line 205:  
This will run overnight.  We will check if it completed at the practical in the morning.
 
This will run overnight.  We will check if it completed at the practical in the morning.
   −
=== Log Out ===
+
==== Log Out ====
 
;Want to log out and leave your job running?
 
;Want to log out and leave your job running?
 
In the screen window, type:
 
In the screen window, type:
Line 225: Line 217:  
exit PuTTY
 
exit PuTTY
   −
=== Wednesday FEEDBACK! ===
+
==== Wednesday FEEDBACK! ====
 
Please provide feedback on the lectures/tutorials from today:  
 
Please provide feedback on the lectures/tutorials from today:  
   Line 234: Line 226:     
<div class="mw-collapsible mw-collapsed" style="width:500px">
 
<div class="mw-collapsible mw-collapsed" style="width:500px">
−
== Thursday Checking if SnpCall Completed ==
+
== Thursday ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
=== Logging Back in to Check Jobs ===
+
=== Checking if SnpCall Completed ===
 +
==== Logging Back in to Check Jobs ====
    
;How do you log back into screen?
 
;How do you log back into screen?
Line 242: Line 235:  
This will resume an already running screen.
 
This will resume an already running screen.
   −
=== Checking Completion ===
+
==== Checking Completion ====
    
Did you get a "completed successfully" message?
 
Did you get a "completed successfully" message?
Line 257: Line 250:       −
== Thursday - Ancestry Tutorial ==
+
=== Ancestry Tutorial ===
 
Now we are going to run the Structural Variation Practical
 
Now we are going to run the Structural Variation Practical
   Line 264: Line 257:  
We will Resume SNP Calling (if necessary) after the practical.
 
We will Resume SNP Calling (if necessary) after the practical.
    +
 +
 +
<div class="mw-collapsible mw-collapsed" style="width:500px">
 +
== Friday ==
 +
<div class="mw-collapsible-content">
    
<div class="mw-collapsible mw-collapsed" style="width:500px">
 
<div class="mw-collapsible mw-collapsed" style="width:500px">
Line 344: Line 342:  
== Friday: Reviewing SNPCALL Results ==
 
== Friday: Reviewing SNPCALL Results ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 +
 +
</div>
 +
</div>
    
</div>
 
</div>
 
</div>
 
</div>
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12283"

Navigation menu