Ns126:Calendar/NOTES/2015-8-31
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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
- Genomic region enrichment analysis
- code File:R20150831.BedEnrichment.txt
- Annotation Database:File:R20150831.BedEnrichment.Annaotation.Database.hg19.txt
- Tissue specific methylation haplotype region analysis
- Dr. Zhang told me to remove H1,Cancer tissues. therefore only 49 sample were included (3 Heyn, 10 N37 and 36 salk) Samples List
- GSI.22.tissues.png
Figure. Heatmap of normal tissues by high GSI regions.
- the methylation haplotype regions in above figure see File:High.gsi.genome.cor.txt
/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