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SeqShop: Association Analysis, May 2015

1,533 bytes removed, 14:05, 19 May 2015
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* Understand how to visualize the association output from EPACTS
== Setup in person at the SeqShop Workshop ==
''This section is specifically for the SeqShop Workshop computers.''
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''If you are not running during the SeqShop Workshop, please skip this section.''
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''If you are not already logged in, please expand this section.''
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{{SeqShopLogin}}
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=== Setup your run environmentPrerequisite Tutorials ===This is the same setup you did for the previous tutorial, but you need to redo it each time you log in. This will setup some environment variables to point you to* [[GotCloud]] program* Tutorial input files* Setup an output directory** It will leave your output directory from the previous tutorial in tact. source /net/seqshop-server/home/mktrost/seqshop/setup.txt* You won't see any output after running <code>source</code>** It silently sets up your environment** If you want to view the detail of the setup, type less /net/seqshop-server/home/mktrost/seqshop/setup.txtand press 'q' to finish. <div class="mw-collapsible mw-collapsed" style="width:200px">View setup.txt<div class="mw-collapsible-content" style="width:800px"> export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud export SS=/net/seqshop-server/home/mktrost/seqshop/example export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts export OUT=~/out mkdir -p ${OUT}</div></div></div></div> == Setup when running on your own outside of the SeqShop Workshop ==''This section is specifically for running on your own outside of the SeqShop Workshop.''<div class="mw-collapsible" style="width:600px">''If you are running during the SeqShop Workshop, please skip this section.''<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]]
cd ~/seqshop/
* download, decompress, and build the version of epacts that was tested with this tutorial:
wget http://wwwcsg.sph.umich.edu/csg/kang/epacts/download/EPACTS-3.2.6.tar.gz
tar xvf EPACTS-3.2.6.tar.gz
cd EPACTS-3.2.6

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