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SeqShop: Association Analysis, May 2015 (view source)

Revision as of 14:15, 21 May 2015

966 bytes removed ,  14:15, 21 May 2015
→‎Download & Build EPACTS
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* Understand how to visualize the association output from EPACTS
 
* Understand how to visualize the association output from EPACTS
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== Setup in person at the SeqShop Workshop ==
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== Setup ==
 
''This section is specifically for the SeqShop Workshop computers.''
 
''This section is specifically for the SeqShop Workshop computers.''
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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<div class="mw-collapsible" style="width:600px">
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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''If you are not already logged in, please expand this section.''
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<div class="mw-collapsible-content">
   
{{SeqShopLogin}}
 
{{SeqShopLogin}}
 
</div>
 
</div>
 
</div>
 
</div>
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=== Setup your run environment===
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=== Prerequisite Tutorials ===
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This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
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 +
This tutorial builds on the alignment & snpcall tutorials, if you have not already, please first run those tutorials: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] & [[SeqShop: Variant Calling and Filtering for SNPs Practical|SNP Calling Tutorial]]
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This will setup some environment variables to point you to
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* [[GotCloud]] program
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* Tutorial input files
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* Setup an output directory
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** It will leave your output directory from the previous tutorial in tact.
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source /net/seqshop-server/home/mktrost/seqshop/setup.txt
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* You won't see any output after running <code>source</code>
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** It silently sets up your environment
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** If you want to view the detail of the setup, type
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less /net/seqshop-server/home/mktrost/seqshop/setup.txt
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and press 'q' to finish.
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<div class="mw-collapsible mw-collapsed" style="width:200px">
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=== Download & Build EPACTS ===
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View setup.txt
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<div class="mw-collapsible-content" style="width:800px">
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export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud
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export SS=/net/seqshop-server/home/mktrost/seqshop/example
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export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts
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export OUT=~/out
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mkdir -p ${OUT}
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</div>
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</div>
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</div>
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</div>
     −
== Setup when running on your own outside of the SeqShop Workshop ==
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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''This section is specifically for running on your own outside of the SeqShop Workshop.''
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''If you are running during the SeqShop Workshop, please skip this section and use EPACTS from Mary Kate's directory.''
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<div class="mw-collapsible" style="width:600px">
  −
''If you are running during the SeqShop Workshop, please skip this section.''
   
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
  −
This tutorial builds on the alignment & snpcall tutorials, if you have not already, please first run those tutorials: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] & [[SeqShop: Variant Calling and Filtering for SNPs Practical|SNP Calling Tutorial]]
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  −
=== Download & Build EPACTS ===
   
If you do not already have EPACTS:
 
If you do not already have EPACTS:
 
* cd to where you want EPACTS installed (you can change this to any directory you want)
 
* cd to where you want EPACTS installed (you can change this to any directory you want)
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  cd ~/seqshop/
 
  cd ~/seqshop/
 
* download, decompress, and build the version of epacts that was tested with this tutorial:
 
* download, decompress, and build the version of epacts that was tested with this tutorial:
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  wget http://www.sph.umich.edu/csg/kang/epacts/download/EPACTS-3.2.6.tar.gz
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  wget http://csg.sph.umich.edu/kang/epacts/download/EPACTS-3.2.6.tar.gz
 
  tar xvf EPACTS-3.2.6.tar.gz
 
  tar xvf EPACTS-3.2.6.tar.gz
 
  cd EPACTS-3.2.6
 
  cd EPACTS-3.2.6
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  make install
 
  make install
 
  cd ../..
 
  cd ../..
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</div>
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</div>
    
{{SeqShopRemoteEnv}}
 
{{SeqShopRemoteEnv}}
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<div class="mw-collapsible" style="width:500px">
 
<div class="mw-collapsible" style="width:500px">
 
<li>Using bash (replace the paths below with the appropriate paths):</li>
 
<li>Using bash (replace the paths below with the appropriate paths):</li>
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<div class="mw-collapsible-content">
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<div class="mw-collapsible" style="width:600px">
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''At the Workshop:''
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<div class="mw-collapsible-content">
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:<pre>export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts</pre>
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</div>
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</div>
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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''Outside of the Workshop:''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
:<pre>export EPACTS=~/seqshop/epacts</pre>
 
:<pre>export EPACTS=~/seqshop/epacts</pre>
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</div>
 +
</div>
 
</div>
 
</div>
 
</div>
 
</div>
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== Return to Workshop Wiki Page ==
 
== Return to Workshop Wiki Page ==
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Return to main workshop wiki page: [[SeqShop: December 2014]]
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Return to main workshop wiki page: [[SeqShop: May 2015]]
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13181...13401"

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