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| | | |
| == Setup == | | == Setup == |
− | <div class="mw-collapsible mw-collapsed" style="width:600px"> | + | <div class="mw-collapsible" style="width:600px"> |
− | ''If you are not already logged in, please expand this section.'' | + | ''If you are already logged in, you can skip this section.'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| {{SeqShopLogin}} | | {{SeqShopLogin}} |
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| Resume screen: | | Resume screen: |
| screen -r | | screen -r |
| + | |
| + | |
| + | <div class="mw-collapsible mw-collapsed" style="width:700px"> |
| + | '''Only if your snpcalling is still running, let Mary Kate know, expand, and follow these instructions''' |
| + | <div class="mw-collapsible-content"> |
| + | * Detach from screen |
| + | Ctrl-a d |
| + | * Start new screen |
| + | screen |
| + | * Reset environment variables (replace SampleXX with your sample name) |
| + | export SAMPLE=SampleXX |
| + | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt |
| + | * When you detach from screen and reattach, you will have multiple screen sessions |
| + | ** The ancestry one will have today's date, the snpcall one will have an earlier date. |
| + | *** Mary Kate can explain how to reattach to a specific session when we get there. |
| + | </div> |
| + | </div> |
| + | |
| + | |
| + | '''Instructions for everyone: Setup LASER''' |
| | | |
| Source the LASER setup: | | Source the LASER setup: |
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| Ctrl-a d | | Ctrl-a d |
| | | |
− | Let's go look at INDEL results: [[SeqShop:_Calling_Your_Own_Genome,_December_2014#Reviewing_Indel_Results|Reviewing Indel Results]]
| + | While that's running, let's go run the Association Analysis Practical: [[SeqShop: Genetic Association Analysis Practical, December 2014]] |
| | | |
| + | === Checking if Pileup finished === |
| + | screen -r |
| + | |
| + | '''Did everyone's finish?''' |
| + | |
| + | |
| + | If not, let's go to Indel: [[SeqShop:_Calling_Your_Own_Genome,_December_2014#Reviewing_Indel_Results]] |
| + | |
| + | |
| + | If yes, let's continue below: |
| === Step 2: pileup --> seq === | | === Step 2: pileup --> seq === |
| | | |
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| | | |
| == Visualizing Ancestry == | | == Visualizing Ancestry == |
− | Copy the R code to plot your ancestry
| |
− | cp -r $LASER/plot/ $OUT/ancestry/.
| |
| | | |
| Change to that new directory: | | Change to that new directory: |
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| Take a look: | | Take a look: |
| evince Results_on_HGDP.pdf & | | evince Results_on_HGDP.pdf & |
− |
| |
| | | |
| == Return to Calling your own Genome == | | == Return to Calling your own Genome == |
− | Go to [[SeqShop: Calling Your Own Genome, December 2014#Friday:_Reviewing_SNPCALL_Results|Reviewing SNPCALL Results]] and pick up where we left off. | + | Go to [[SeqShop:_Calling_Your_Own_Genome,_December_2014#Reviewing_Indel_Results]] and pick up where we left off. |