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SeqShop: Calling Your Own Genome, May 2015 (view source)

Revision as of 09:44, 22 May 2015

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== Thursday ==
 
== Thursday ==
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== Friday ==
 
== Friday ==
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[[SeqShop: Ancestry On Your Own Genome, May 2015]]
 
[[SeqShop: Ancestry On Your Own Genome, May 2015]]
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=== Association Analysis Tutorial ===
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=== Setup Variables ===
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Now we are going to run the Association Analysis Practical
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Set these values.  Also, be sure to specify your sample name instead of SampleXX
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export SAMPLE=SampleXX
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or
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export SAMPLE=NA12878
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Please go to: [[SeqShop: Association Analysis, May 2015]]
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Point to your GotCloud & your output directory:
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export GC=~/seqshop/gotcloud
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We will look at our own genomes again after the practical.
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export OUT=~/$SAMPLE/output
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=== Return to SeqShop: Ancestry On Your Own Genome, May 2015 ===
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Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_May_2015#Checking_if_Pileup_finished]]
      
=== Reviewing Indel Results ===
 
=== Reviewing Indel Results ===
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Set these values.  Also, be sure to specify your sample name (or NA12878) instead of SampleXX
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export SAMPLE=SampleXX
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source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
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Look in the output directory
 
Look in the output directory
 
  ls ~/$SAMPLE/output
 
  ls ~/$SAMPLE/output
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The insertion deletion ratio increases from 0.91 to 0.92.   
 
The insertion deletion ratio increases from 0.91 to 0.92.   
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=== Return to SeqShop: Ancestry On Your Own Genome, May 2015 ===
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Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_May_2015#Checking_if_Pileup_finished]]
    
=== Friday: Reviewing SNPCALL Results ===
 
=== Friday: Reviewing SNPCALL Results ===
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=== Friday : More SNP Analysis ===
 
=== Friday : More SNP Analysis ===
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==== Environmental Variables ====
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If you didn't set the environmental variable, you can set it again
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export SAMPLE=SampleXX (MAKE SURE TO CHANGE XX to your number or use NA12878 instead)
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export OUT=~/$SAMPLE/output
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In addition, set another environmental variable for locating the binaries for custom analysis
 
In addition, set another environmental variable for locating the binaries for custom analysis
    
  export HK=/net/seqshop-server/home/hmkang/apigenome/bin
 
  export HK=/net/seqshop-server/home/hmkang/apigenome/bin
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export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/
    
==== Annotation / Lookup against dbSNP ====
 
==== Annotation / Lookup against dbSNP ====
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13426"

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