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| '''Setup LASER''' | | '''Setup LASER''' |
| export SSREF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref | | export SSREF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref |
− | export LASER=$OUT/ancestry/LASER-2.01 | + | export LASER=~/seqshop/output/ancestry/LASER-2.01 |
− | (SAMPLE & OUT were previously set in your screen session.) | + | (SAMPLE were previously set in your screen session.) |
| | | |
| After setting this, also do | | After setting this, also do |
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| Ctrl-a d | | Ctrl-a d |
| | | |
− | While that's running, let's go run the Association Analysis Practical: [[SeqShop: Genetic Association Analysis Practical, December 2014]] | + | While that's running, let's go look at Calling results: [[ SeqShop: Calling Your Own Genome, May 2015]] |
| | | |
| === Checking if Pileup finished === | | === Checking if Pileup finished === |
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| | | |
| python $LASER/pileup2seq/pileup2seq.py \ | | python $LASER/pileup2seq/pileup2seq.py \ |
− | -m $SSREF/HGDP_938.site \ | + | -m $SSREF/HGDP/HGDP_938.site \ |
| -o $OUT/ancestry/$SAMPLE.HGDP \ | | -o $OUT/ancestry/$SAMPLE.HGDP \ |
| $OUT/ancestry/$SAMPLE.HGDP.pileup | | $OUT/ancestry/$SAMPLE.HGDP.pileup |
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| This step will take about 5-6 minutes. | | This step will take about 5-6 minutes. |
| | | |
− | $LASER/laser -g $SSREF/HGDP_938.geno -c $SSREF/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP & | + | $LASER/laser -g $SSREF/HGDP/HGDP_938.geno -c $SSREF/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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| | | |
| Generate the plot: | | Generate the plot: |
− | Rscript plotHGDP.r $HGDP/HGDP_938.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP.SeqPC.coord | + | Rscript plotHGDP.r $SSREF/HGDP/HGDP_938.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP.SeqPC.coord |
| | | |
| Take a look: | | Take a look: |
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| | | |
| For European ancestry: | | For European ancestry: |
− | $LASER/laser -g $HGDP/HGDP.633K.euro.geno -c $HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-Euro & | + | $LASER/laser -g $SSREF/HGDP/HGDP.633K.euro.geno -c $SSREF/HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-Euro & |
| | | |
| For East Asian ancestry: | | For East Asian ancestry: |
− | $LASER/laser -g $HGDP/HGDP.633K.easia.2.geno -c $HGDP/HGDP.633K.easia.2.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-EAsia & | + | $LASER/laser -g $SSREF/HGDP/HGDP.633K.easia.2.geno -c $SSREF/HGDP/HGDP.633K.easia.2.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-EAsia & |
| | | |
| For Central/South Asian ancestry: | | For Central/South Asian ancestry: |
− | $LASER/laser -g $HGDP/HGDP.633K.csasia.2.geno -c $HGDP/HGDP.633K.csasia.2.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-CSAsia & | + | $LASER/laser -g $SSREF/HGDP/HGDP.633K.csasia.2.geno -c $SSREF/HGDP/HGDP.633K.csasia.2.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-CSAsia & |
| | | |
| | | |
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| | | |
| Generate the plot for European ancestry: | | Generate the plot for European ancestry: |
− | Rscript plotHGDP.r $HGDP/HGDP.633K.euro.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-Euro.SeqPC.coord | + | Rscript plotHGDP.r $SSREF/HGDP/HGDP.633K.euro.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-Euro.SeqPC.coord |
| or for East Asian ancestry | | or for East Asian ancestry |
− | Rscript plotHGDP.r $HGDP/HGDP.633K.easia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-EAsia.SeqPC.coord | + | Rscript plotHGDP.r $SSREF/HGDP/HGDP.633K.easia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-EAsia.SeqPC.coord |
| or for Central/South Asian ancestry | | or for Central/South Asian ancestry |
− | Rscript plotHGDP.r $HGDP/HGDP.633K.csasia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-CSAsia.SeqPC.coord | + | Rscript plotHGDP.r $SSREF/HGDP/HGDP.633K.csasia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-CSAsia.SeqPC.coord |
| | | |
| Take a look: | | Take a look: |