Changes

From Genome Analysis Wiki
Jump to navigationJump to search
Line 47: Line 47:  
''If you are running during the SeqShop Workshop, please skip this section.''
 
''If you are running during the SeqShop Workshop, please skip this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
=== Download the example data ===
     −
=== Setup your run environment ===
+
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
   −
Environment variables will be used throughout the tutorial.
+
It also uses the bam.index file created in the SnpCall Tutorial.  If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#GotCloud_BAM_Index_File|GotCloud BAM Index File]]
   −
We recommend that you setup these variables so you won't have to modify every command in the tutorial.
     −
<div class="mw-collapsible mw-collapsed" style="width:500px">
+
{{SeqShopRemoteEnv}}
I'm using bash (replace the paths below with the appropriate paths):
  −
<div class="mw-collapsible-content">
  −
* Point to where you installed GotCloud
  −
*:<pre>export GC=/home/username/gotcloud</pre>
  −
* Point to where you installed the seqshop files
  −
*:<pre>export SS=/home/username/seqshop/</pre>
  −
* Point to where you want the output to go
  −
*:<pre>export OUT=/home/username/seqshop_output/</pre>
   
</div>
 
</div>
 
</div>
 
</div>
  −
<div class="mw-collapsible mw-collapsed" style="width:500px">
  −
I'm using tcsh (replace the paths below with the appropriate paths):
  −
<div class="mw-collapsible-content">
  −
* Point to where you installed GotCloud
  −
*:<pre>setenv GC /home/username/gotcloud</pre>
  −
* Point to where you installed the seqshop files
  −
*:<pre>setenv SS /home/username/seqshop/</pre>
  −
* Point to where you want the output to go
  −
*:<pre>setenv OUT /home/username/seqshop_output/</pre>
  −
</div>
  −
</div>
  −
  −
</div>
  −
</div>
  −
      
== Examining GotCloud/GenomeSTRiP Input files ==
 
== Examining GotCloud/GenomeSTRiP Input files ==

Navigation menu