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SeqShop: Sequence Mapping and Assembly Practical, June 2014 (view source)

Revision as of 11:07, 2 February 2017

883 bytes removed ,  11:07, 2 February 2017
→‎Download the example data
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'''Note:''' the latest version of this practical is available at: [[SeqShop: Sequence Mapping and Assembly Practical]]
 +
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
 +
 
== Introduction ==
 
== Introduction ==
 
See the [[Media:SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
 
See the [[Media:SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
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=== Download the example data ===
 
=== Download the example data ===
 
Download and untar file containing the example data used in the practicals:
 
Download and untar file containing the example data used in the practicals:
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  wget http://www.sph.umich.edu/csg/mktrost/seqshopExample.tar.gz
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  wget http://csg.sph.umich.edu//mktrost/seqshopExample.tar.gz
 
  tar xvf seqshopExample.tar.gz
 
  tar xvf seqshopExample.tar.gz
    
You will see the names of all the files included in the example data scrolling on the screen as they are unpacked from the tar file.
 
You will see the names of all the files included in the example data scrolling on the screen as they are unpacked from the tar file.
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=== Setup your run environment ===
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{{SeqShopRemoteEnv}}
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  −
Environment variables will be used throughout the tutorial.
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  −
We recommend that you setup these variables so you won't have to modify every command in the tutorial.
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  −
 
  −
<div class="mw-collapsible mw-collapsed" style="width:500px">
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Using bash (replace the paths below with the appropriate paths):
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<div class="mw-collapsible-content">
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* Point to where you installed GotCloud
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*:<pre>export GC=~/seqshop/gotcloud</pre>
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* Point to where you installed the seqshop files
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*:<pre>export SS=~/seqshop/example</pre>
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* Point to where you want the output to go
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*:<pre>export OUT=~/seqshop/output</pre>
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</div>
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</div>
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<div class="mw-collapsible mw-collapsed" style="width:500px">
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Using tcsh (replace the paths below with the appropriate paths):
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<div class="mw-collapsible-content">
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* Point to where you installed GotCloud
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*:<pre>setenv GC ~/seqshop/gotcloud</pre>
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* Point to where you installed the seqshop files
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*:<pre>setenv SS ~/seqshop/example</pre>
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* Point to where you want the output to go
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*:<pre>setenv OUT ~/seqshop/output</pre>
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</div>
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</div>
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</div>
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</div>
      
== Examining [[GotCloud]] Align Input Files ==
 
== Examining [[GotCloud]] Align Input Files ==
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<li>View Screenshot</li>
 
<li>View Screenshot</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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[[File:RefDir.png|500px]]
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[[File:RefDir.png|700px]]
 
</div>
 
</div>
 
</div>
 
</div>
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<li>Need a reminder of the format?</li>
 
<li>Need a reminder of the format?</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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[[File:fqindex.png|650px]]
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[[File:fqindex.png|750px]]
 
</div>
 
</div>
 
</div>
 
</div>
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<li>HG00553 & HG00640</li>
 
<li>HG00553 & HG00640</li>
 
<li>They have multiple unique values in the RGID field</li>
 
<li>They have multiple unique values in the RGID field</li>
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[[File:fqindexRG.png|650px]]
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[[File:fqindexRG.png|800px]]
 
</div>
 
</div>
 
</div>
 
</div>
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Use the <code>space bar</code> to advance if the whole file isn't displayed.
 
Use the <code>space bar</code> to advance if the whole file isn't displayed.
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; If your input and references are at different paths than specified, what would you change?
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; If your references are in a different path than what is specified, what would you change?
 
<ul>
 
<ul>
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<div class="mw-collapsible mw-collapsed" style="width:200px">
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<div class="mw-collapsible mw-collapsed" style="width:300px">
 
<li>Answer:</li>
 
<li>Answer:</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
<ul>
 
<ul>
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<li>You would change <code>IN_DIR</code> & <code>REF_DIR</code> to the new paths</li>
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<li>You would change <code>REF_DIR</code> to the new path</li>
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[[File:gcConf.png|500px]]
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[[File:gcConf.png|800px]]
 
</div>
 
</div>
 
</div>
 
</div>
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[[File:Qplotpdf.png|400px]]
 
[[File:Qplotpdf.png|400px]]
 
<li> Look at the PDF I produced when I ran the whole genome:</li>  
 
<li> Look at the PDF I produced when I ran the whole genome:</li>  
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  evince ${SS}/example/HG00551.wg.qplot.pdf&
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  evince ${SS}/ext/HG00551.wg.qplot.pdf&
 
</ul>
 
</ul>
 
[[File:Qplotpdfwg.png|400px]]
 
[[File:Qplotpdfwg.png|400px]]
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