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

Revision as of 11:07, 2 February 2017

299 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]]
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* The ones here is the original one from the June workshop (updated to be run from elsewhere)
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== 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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If you do not already have GotCloud:
 
If you do not already have GotCloud:
 
* cd to where you want GotCloud installed (you can change this to any directory you want)
 
* cd to where you want GotCloud installed (you can change this to any directory you want)
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mkdir -p ~/seqshop
 
  cd ~/seqshop/
 
  cd ~/seqshop/
 
* 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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=== Download the example data ===
 
=== Download the example data ===
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Download and untar file containing the example data used in the practicals:
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wget http://csg.sph.umich.edu//mktrost/seqshopExample.tar.gz
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tar xvf seqshopExample.tar.gz
   −
=== Setup your run environment ===
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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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  −
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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{{SeqShopRemoteEnv}}
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<div class="mw-collapsible mw-collapsed" style="width:500px">
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I'm 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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I'm 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>
  −
 
  −
</div>
  −
</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.
   −
; 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 ${IN}/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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== Logging Off ==
 
== Logging Off ==
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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">
 
To logout of seqshop-server, type:
 
To logout of seqshop-server, type:
 
  exit
 
  exit
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When done, log out of the Windows machine.
 
When done, log out of the Windows machine.
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</div>
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</div>
Ppwhite
96

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