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240 bytes added
, 14:32, 13 November 2014
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| + | '''Note:''' the latest version of this practical is available at: [[SeqShop: Ancestry On Your Own Genome]] |
| + | * The ones here is the original one from the June workshop (updated to be run from elsewhere) |
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| {{SeqShopLogin}} | | {{SeqShopLogin}} |
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| OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately: | | OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately: |
| export OUT=~/personal/YOUR_OUTPUT_DIR | | export OUT=~/personal/YOUR_OUTPUT_DIR |
| + | After setting this, also do |
| + | mkdir -p $OUT/ancestry |
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| Verify that this does not give an error: | | Verify that this does not give an error: |
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| -m $HGDP/HGDP_938.site \ | | -m $HGDP/HGDP_938.site \ |
| -o $OUT/ancestry/$SAMPLE.laser \ | | -o $OUT/ancestry/$SAMPLE.laser \ |
− | $OUT/ancestry/Sample_37224.recal.pileup | + | $OUT/ancestry/$SAMPLE.recal.pileup |
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| This step takes just a few seconds. | | This step takes just a few seconds. |
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| View the results: | | View the results: |
− | less -S $OUT/ancestry/Sample_37224.laser.1.SeqPC.coord | + | less -S $OUT/ancestry/${SAMPLE}.laser.2.SeqPC.coord |
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| == Visualizing Ancestry == | | == Visualizing Ancestry == |
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| Generate the plot: | | Generate the plot: |
− | Rscript plotHGDP.r $HGDP/HGDP_938.RefPC.coord $OUT/ancestry/Sample_37224.laser.1.SeqPC.coord | + | Rscript plotHGDP.r $HGDP/HGDP_938.RefPC.coord $OUT/ancestry/${SAMPLE}.laser.2.SeqPC.coord |
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| Take a look: | | Take a look: |
| evince Results_on_HGDP.pdf & | | evince Results_on_HGDP.pdf & |
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| ==Interested in looking just at European populations?== | | ==Interested in looking just at European populations?== |
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| -m $HGDP/HGDP.633K.euro.site \ | | -m $HGDP/HGDP.633K.euro.site \ |
| -o $OUT/ancestry/$SAMPLE.Euro.laser \ | | -o $OUT/ancestry/$SAMPLE.Euro.laser \ |
− | $OUT/ancestry/Sample_37224.recal.pileup | + | $OUT/ancestry/${SAMPLE}.recal.pileup |
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| This step takes just a few seconds. | | This step takes just a few seconds. |