Ns126:Calendar/NOTES/2015-8-31: Difference between revisions
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** Annotation Database:[[File:R20150831.BedEnrichment.Annaotation.Database.hg19.txt]] | ** Annotation Database:[[File:R20150831.BedEnrichment.Annaotation.Database.hg19.txt]] | ||
* Tissue specific methylation haplotype region analysis | * Tissue specific methylation haplotype region analysis | ||
*[[Samples List]] | * Dr. Zhang told me to remove H1,Cancer tissues. therefore only 49 sample were included (3 Heyn, 10 N37 and 36 salk) [[Samples List]] | ||
*[[File:Code.20190903.TSI.22.tissues.R.txt]] | *[[File:Code.20190903.TSI.22.tissues.R.txt]] |
Revision as of 17:50, 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
- 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)