Ns126:Calendar/NOTES/2016-2-18: Difference between revisions

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>Shicheng
>Shicheng
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===purpose==
===purpose==
# plot MHB heatmap block
plot MHB heatmap block


===Method===
===Method===
 
*Bam2haploinfo from GWBS dataset
# Bam2haploinfo from GWBS dataset
*Merge All the haploinfo files
 
 
# 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
*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
*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

Result