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| </div> | | </div> |
| | | |
− | <div class="mw-collapsible" style="width:500px"> | + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| | | |
| == Thursday == | | == Thursday == |
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| </div> | | </div> |
| | | |
− | <div class="mw-collapsible mw-collapsed" style="width:1000px"> | + | <div class="mw-collapsible" style="width:1000px"> |
| | | |
| == Friday == | | == Friday == |
− | <div class="mw-collapsible-content mw-collapsed"> | + | <div class="mw-collapsible-content"> |
| | | |
| | | |
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| [[SeqShop: Ancestry On Your Own Genome, May 2015]] | | [[SeqShop: Ancestry On Your Own Genome, May 2015]] |
| | | |
− | === Association Analysis Tutorial === | + | === Setup Variables === |
− | Now we are going to run the Association Analysis Practical
| + | Set these values. Also, be sure to specify your sample name instead of SampleXX |
| + | export SAMPLE=SampleXX |
| + | or |
| + | export SAMPLE=NA12878 |
| | | |
− | Please go to: [[SeqShop: Association Analysis, May 2015]]
| + | Point to your GotCloud & your output directory: |
− | | + | export GC=~/seqshop/gotcloud |
− | We will look at our own genomes again after the practical.
| + | export OUT=~/$SAMPLE/output |
− | | |
− | === Return to SeqShop: Ancestry On Your Own Genome, May 2015 ===
| |
− | Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_May_2015#Checking_if_Pileup_finished]]
| |
| | | |
| === Reviewing Indel Results === | | === Reviewing Indel Results === |
− | Set these values. Also, be sure to specify your sample name (or NA12878) instead of SampleXX
| |
− | export SAMPLE=SampleXX
| |
− | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
| |
− |
| |
| Look in the output directory | | Look in the output directory |
| ls ~/$SAMPLE/output | | ls ~/$SAMPLE/output |
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| The insertion deletion ratio increases from 0.91 to 0.92. | | The insertion deletion ratio increases from 0.91 to 0.92. |
| | | |
| + | === Return to SeqShop: Ancestry On Your Own Genome, May 2015 === |
| + | Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_May_2015#Checking_if_Pileup_finished]] |
| | | |
| === Friday: Reviewing SNPCALL Results === | | === Friday: Reviewing SNPCALL Results === |
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| | | |
| === Friday : More SNP Analysis === | | === Friday : More SNP Analysis === |
− |
| |
− | ==== Environmental Variables ====
| |
− |
| |
− | If you didn't set the environmental variable, you can set it again
| |
− |
| |
− | export SAMPLE=SampleXX (MAKE SURE TO CHANGE XX to your number or use NA12878 instead)
| |
− | export OUT=~/$SAMPLE/output
| |
− |
| |
| 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 |
| + | export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/ |
| | | |
| ==== Annotation / Lookup against dbSNP ==== | | ==== Annotation / Lookup against dbSNP ==== |