Ns126:Calendar/NOTES/2015-8-31: Difference between revisions
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*[[Samples List]] | *[[Samples List]] | ||
[[File:GSI.22.tissues.png| | [[File:GSI.22.tissues.png|400px]] | ||
[[File:Code.20190903.TSI.22.tissues.R.txt]] | [[File:Code.20190903.TSI.22.tissues.R.txt]] | ||
Revision as of 04:20, 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
- Samples List
File:GSI.22.tissues.png File:Code.20190903.TSI.22.tissues.R.txt
- Density.CorrelationDifferenceBetweenCancerNormal.jpg
Figure 2. Density plot for the correlation of high density CpG regions in 450K array between cancer and normals
- CorrelationDifferenceBetweenCancerNormal.jpg
Figure 3. Comparison of the correlation for the high density CpG regions in 450K array between cancer and normals
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 discuss with Dinh, the methylFreq files of 106 samples were collected (10 N37, 36 Salk, 57 MONOD and 3 Heyn2013Age)