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SeqShop: Association Analysis, May 2015 (view source)

Revision as of 15:05, 19 May 2015

1,533 bytes removed ,  15:05, 19 May 2015
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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 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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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>
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== Setup when running on your own outside of the SeqShop Workshop ==
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''This section is specifically for running on your own outside of the SeqShop Workshop.''
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<div class="mw-collapsible" style="width:600px">
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''If you are running during the SeqShop Workshop, please skip this section.''
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<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]]
 
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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  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
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13366"

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