Ns126:Calendar/NOTES/2015-8-31: Difference between revisions

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*the methylation haplotype regions in above figure see [[File:High.gsi.genome.cor.txt]]
*the methylation haplotype regions in above figure see [[File:High.gsi.genome.cor.txt]]
/home/sguo/monod/phase2/high.gsi.genome.cor.txt
*





Revision as of 06:42, 23 September 2015


  • liftover epigenetic annotation from hg18 to hg19
./liftOver Hic.topological.domain.hESC.hg18.bed hg18ToHg19.over.chain Hic.topological.domain.hESC.hg19.bed tmp
./liftOver Hic.topological.domain.IMR90.hg18.bed  hg18ToHg19.over.chain Hic.topological.domain.IMR90.hg19.bed tmp
./liftOver Hic.boundary.IMR90.hg18.bed hg18ToHg19.over.chain Hic.boundary.IMR90.hg19.bed tmp
./liftOver Hic.boundary.hESC.hg18.bed hg18ToHg19.over.chain Hic.boundary.hESC.hg19.bed tmp
./liftOver Hic.common.boundary.hESC.IMR90.hg18.bed hg18ToHg19.over.chain Hic.common.boundary.hESC.IMR90.hg19.bed tmp
/home/sguo/monod/phase2/high.gsi.genome.cor.txt


compare the cluster analysis with raw methylation signal

Achieve raw methylFreq files

  • I found the overlapped CpG sites between methylation haplotype and raw methylFreq (depth>5) was only 49. The reason when we calculate the methylation haplotype we did not get rid of low coverage reads. Therefore, I need collect the raw methylation methylFreq file and merage them again without low coverage reads discarding.
  • After discussing with Dinh, the methylFreq files of 106 samples were collected (10 N37, 36 Salk, 57 MONOD and 3 Heyn2013Age)