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

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* Partial CpG Mode Figure  
* Partial CpG Mode Figure  
[[File:APC.LD.block-2.jpg|50*50]]
[[File:APC.LD.block-2.jpg|50*50]]
* Full CpG mode Figure
* Full CpG mode Figure
[[File:APC.LD.block-1.jpg|50*50]]

Revision as of 09:55, 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

  • Partial CpG Mode Figure

50*50

  • Full CpG mode Figure

50*50