Ns126:Calendar/NOTES/2015-8-31: Difference between revisions
Jump to navigation
Jump to search
>Shicheng No edit summary |
>Shicheng No edit summary |
||
Line 23: | Line 23: | ||
== compare the cluster analysis with raw methylation signal== | == 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. | *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) | *After discuss with Dinh, the methylFreq files of 106 samples were collected (10 N37, 36 Salk, 57 MONOD and 3 Heyn2013Age) |
Revision as of 04:30, 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
- GSI.22.tissues.png
Figure. Heatmap of normal tissues by high GSI regions.
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)