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| + | __TOC__ |
| + | |
| + | == Setup == |
| + | <div class="mw-collapsible" style="width:600px"> |
| + | ''If you are already logged in, you can skip this section.'' |
| + | <div class="mw-collapsible-content"> |
| {{SeqShopLogin}} | | {{SeqShopLogin}} |
| + | </div> |
| + | </div> |
| + | |
| + | == Setup your terminal == |
| + | |
| + | Resume screen: |
| + | screen -r |
| + | |
| | | |
− | == Setup == | + | <div class="mw-collapsible mw-collapsed" style="width:700px"> |
− | ''If you were sequenced, set these values:'' | + | '''Only if your snpcalling is still running, let Mary Kate know, expand, and follow these instructions''' |
− | export SAMPLE=Sample* | + | <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 | | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt |
− | source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.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''' |
| | | |
− | ''If you were not sequenced, set these values:''
| + | Source the LASER setup: |
− | export SAMPLE=NA12878
| |
− | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
| |
| source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt | | source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt |
| + | (SAMPLE & OUT were previously set in your screen session.) |
| | | |
| After setting this, also do | | After setting this, also do |
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| This step takes ~1 hour for a genome sequenced at 17X. | | This step takes ~1 hour for a genome sequenced at 17X. |
| | | |
| + | While this is running, we will go look at other results, so exit screen: |
| + | Ctrl-a d |
| + | |
| + | 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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| This step will take about 5-6 minutes. | | This step will take about 5-6 minutes. |
| | | |
− | $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.laser.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP & | + | $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP & |
| | | |
| View the results: | | View the results: |
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| 8 European populations in the HGDP dataset, including 156 individuals in total. | | 8 European populations in the HGDP dataset, including 156 individuals in total. |
| | | |
− | 17 East Asian populations in the HGDP dataset, including 215 individuals after excluding 4 outliers (defined as more than 5 standard deviations from mean in any of top 10 PCs, 1 removal iteration).
| + | 18 East Asian populations in the HGDP dataset, including 224 individuals after excluding 5 outliers (defined as more than 5 standard deviations from mean in any of top 10 PCs, 1 removal iteration). |
| | | |
| 8 Central/South Asian populations in the HGDP dataset, including 195 individuals after excluding 5 outliers (defined as more than 5 standard deviations from mean in any of top 10 PCs, 1 removal iteration). Note that 7 out of these 8 population were collected in Pakistan and 1 was collected in China (Uygur). | | 8 Central/South Asian populations in the HGDP dataset, including 195 individuals after excluding 5 outliers (defined as more than 5 standard deviations from mean in any of top 10 PCs, 1 removal iteration). Note that 7 out of these 8 population were collected in Pakistan and 1 was collected in China (Uygur). |
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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 == |
| + | Go to [[SeqShop:_Calling_Your_Own_Genome,_December_2014#Reviewing_Indel_Results]] and pick up where we left off. |