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Revision as of 14:25, 13 November 2014
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'''Note:''' the latest version of this practical is available at: [[SeqShop: Aligning Your Own Genome]]
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
== First Things First ==
== First Things First ==
*Helpful reference to many tools:
*Helpful reference to many tools:
perl /home/mktrost/seqshop/inputs/buildIndex.pl ~/personal > ~/personal/align.2x.index
perl /home/mktrost/seqshop/inputs/buildIndex.pl ~/personal > ~/personal/align.2x.index
* <code>></code> means to direct the output to the file specified after the <code>></code>
* <code>></code> means to direct the output to the file specified after the <code>></code>
Curious what the script looks like and what it does in case you want to create one in the future?
<div class="mw-collapsible mw-collapsed" style="width:200px">
<li>View Annotated Script</li>
<div class="mw-collapsible-content">
[[File:BuildIndex.png|800px]]
</div>
</div>
=== Checking your index file listing your FASTQs ===
=== Checking your index file listing your FASTQs ===
