Ns126:Calendar/NOTES/2016-2-18: Difference between revisions
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>Shicheng (→Method) |
>Shicheng |
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===purpose== | ===purpose== | ||
plot MHB heatmap block | |||
===Method=== | ===Method=== | ||
*Bam2haploinfo from GWBS dataset | |||
*Merge All the haploinfo files | |||
cd /home/shg047/oasis/monod/haplo/ | cd /home/shg047/oasis/monod/haplo/ | ||
cat /home/shg047/oasis/monod/haplo/n37/*hapInfo.txt >> hapinfo.txt | cat /home/shg047/oasis/monod/haplo/n37/*hapInfo.txt >> hapinfo.txt | ||
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cat /home/shg047/oasis/monod/haplo/tumor_wgbs/*hapInfo.txt >> hapinfo.txt | cat /home/shg047/oasis/monod/haplo/tumor_wgbs/*hapInfo.txt >> hapinfo.txt | ||
cat /home/shg047/oasis/monod/haplo/salk/*hapInfo.txt >> hapinfo.txt | cat /home/shg047/oasis/monod/haplo/salk/*hapInfo.txt >> hapinfo.txt | ||
*Haploinfo to R-square matrix by Genomic Region | |||
cd /home/shg047/oasis/monod/haplo/ | cd /home/shg047/oasis/monod/haplo/ | ||
perl [[~/oasis/monod/bin/haploinfo2LDR2.pl]] APC chr5:111986595-112228720 < /home/shg047/oasis/monod/haplo/hapinfo.txt | perl [[~/oasis/monod/bin/haploinfo2LDR2.pl]] APC chr5:111986595-112228720 < /home/shg047/oasis/monod/haplo/hapinfo.txt | ||
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perl ~/oasis/monod/bin/haploinfo2LDR2.pl SHOX2 chr3:157808200-157829413 < /home/shg047/oasis/monod/haplo/hapinfo.txt | perl ~/oasis/monod/bin/haploinfo2LDR2.pl SHOX2 chr3:157808200-157829413 < /home/shg047/oasis/monod/haplo/hapinfo.txt | ||
perl ~/oasis/monod/bin/haploinfo2LDR2.pl DIRAS3 chr1:68511645-68516481 < /home/shg047/oasis/monod/haplo/hapinfo.txt | perl ~/oasis/monod/bin/haploinfo2LDR2.pl DIRAS3 chr1:68511645-68516481 < /home/shg047/oasis/monod/haplo/hapinfo.txt | ||
*Extent Full R-square matrix by Human Genome CpG sites | |||
perl [[/home/shg047/oasis/monod/bin/LDR2extent.pl]] chr5:112039140-112047142 APC.chr5.sqr > APC.full.region.sqr | perl [[/home/shg047/oasis/monod/bin/LDR2extent.pl]] chr5:112039140-112047142 APC.chr5.sqr > APC.full.region.sqr | ||
=== Result === | === Result === |
Revision as of 09:44, 26 February 2016
Methylation Haplotype Block Plot
=purpose
plot MHB heatmap block
Method
- Bam2haploinfo from GWBS dataset
- Merge All the haploinfo files
cd /home/shg047/oasis/monod/haplo/ cat /home/shg047/oasis/monod/haplo/n37/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/wbc/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/hesc/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/tumor_wgbs/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/salk/*hapInfo.txt >> hapinfo.txt
- Haploinfo to R-square matrix by Genomic Region
cd /home/shg047/oasis/monod/haplo/ perl ~/oasis/monod/bin/haploinfo2LDR2.pl APC chr5:111986595-112228720 < /home/shg047/oasis/monod/haplo/hapinfo.txt perl ~/oasis/monod/bin/haploinfo2LDR2.pl ZNF154 chr19:58206356-58222715 < /home/shg047/oasis/monod/haplo/hapinfo.txt perl ~/oasis/monod/bin/haploinfo2LDR2.pl SHOX2 chr3:157808200-157829413 < /home/shg047/oasis/monod/haplo/hapinfo.txt perl ~/oasis/monod/bin/haploinfo2LDR2.pl DIRAS3 chr1:68511645-68516481 < /home/shg047/oasis/monod/haplo/hapinfo.txt
- Extent Full R-square matrix by Human Genome CpG sites
perl /home/shg047/oasis/monod/bin/LDR2extent.pl chr5:112039140-112047142 APC.chr5.sqr > APC.full.region.sqr