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

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* Bam to methyhaplotype
* Bam to methyhaplotype
* I found a problem, I do not know why not CG would occur in methyhplot and why position would occur multiple time.
* I found a problem, I do not know why not CG would occur in methyhplot and why position would occur multiple time. You can try the following command:
  grep chr6:53658269-53659397 /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/BSPP/mld_block_stringent_hapInfo/NC-23.WGBS_BSPP.mld_blocks_r2-0.5.hapInfo.txt
  grep chr6:53658269-53659397 /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/BSPP/mld_block_stringent_hapInfo/NC-23.WGBS_BSPP.mld_blocks_r2-0.5.hapInfo.txt

Revision as of 00:48, 25 September 2015


Compare methylation haplotype region with Hic Data

  • 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)
  • 651 CpG sites were found overlapped with 180 high GSI methylation haplotype regions. among them, 35 sites were found have more than 30% missing value and then were filtered in the further analysis.
  • the heatmap based on raw methylation signals were as the following(right). File:Heatmap.RawSignal.High.GSI.R.txt

File:GSI.RRBS.BSPP.WGBS.RawSignal.png

Comare MHL and Average methylation level

  • Bam to methyhaplotype
  • I found a problem, I do not know why not CG would occur in methyhplot and why position would occur multiple time. You can try the following command:
grep chr6:53658269-53659397 /home/kunzhang/CpgMIP/MONOD/Data/150209_SN216/BSPP/mld_block_stringent_hapInfo/NC-23.WGBS_BSPP.mld_blocks_r2-0.5.hapInfo.txt