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SeqShop: Sequence Mapping and Assembly Practical, May 2015 (view source)

Revision as of 03:00, 28 January 2016

692 bytes removed ,  03:00, 28 January 2016
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Main Workshop wiki page: [[SeqShop: May 2015]]
 
Main Workshop wiki page: [[SeqShop: May 2015]]
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See the [[Media:Dec2014 SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
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See the [[Media:May2015 SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
    
== Goals of This Session ==
 
== Goals of This Session ==
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** How to visualize sequence data to examine the reads aligned to particular genomic positions
 
** How to visualize sequence data to examine the reads aligned to particular genomic positions
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== Setup in person at the SeqShop Workshop ==
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== Setup ==
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''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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''If you are not running during the SeqShop Workshop, please skip this section.''
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<div class="mw-collapsible-content">
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{{SeqShopLogin}}
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=== Setup your run environment===
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This will setup some environment variables to point you to
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''The section below is specifically for the Michigan SeqShop Workshop computers.''
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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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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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Look at setup.txt
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<div class="mw-collapsible mw-collapsed">
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cat /net/seqshop-server/home/mktrost/seqshop/setup.txt
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''If you are using a SeqShop computer, please expand this section.''
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<div class="mw-collapsible mw-collapsed" style="width:200px">
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* setup.txt screenshot
   
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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[[File:setup.png|500px]]
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{{SeqShopLoginA}}
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</div>
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</div>
   
</div>
 
</div>
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</div>
 
</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">
      
=== Download the example data ===
 
=== Download the example data ===
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If you do not already have GotCloud:
 
If you do not already have GotCloud:
 
* download, decompress, and build the version of gotcloud that was tested with this tutorial:
 
* download, decompress, and build the version of gotcloud that was tested with this tutorial:
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  wget https://github.com/statgen/gotcloud/archive/gotcloud.1.17.tar.gz
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  wget https://github.com/statgen/gotcloud/archive/gotcloud.1.17.4.tar.gz
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  tar xvf gotcloud.1.17.tar.gz
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  tar xvf gotcloud.1.17.4.tar.gz
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  mv gotcloud-gotcloud.1.17 gotcloud
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  mv gotcloud-gotcloud.1.17.4 gotcloud
 
  cd gotcloud/src
 
  cd gotcloud/src
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  make
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  make -j 3
 
  cd ../..
 
  cd ../..
    
Remember the path to gotcloud/ that is what you will need to set your GC variable to.
 
Remember the path to gotcloud/ that is what you will need to set your GC variable to.
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{{SeqShopRemoteEnv}}
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''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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''If you are using a SeqShop computer, please expand this section.''
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<div class="mw-collapsible-content">
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{{SeqShopLoginSubMachine}}
 
</div>
 
</div>
 
</div>
 
</div>
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{{SeqShopRemoteEnv}}
    
== Examining [[GotCloud]] Align Input Files ==
 
== Examining [[GotCloud]] Align Input Files ==
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''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 mw-collapsed">
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''If you are not running during the SeqShop Workshop, please skip this section.''
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''If you are running on a SeqShop computer, please expand this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
To logout of seqshop1/2/3/4, type:
 
To logout of seqshop1/2/3/4, type:
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13266...14059"

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