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

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*[[File:Code.20190903.TSI.22.tissues.R.txt]]
*[[File:Code.20190903.TSI.22.tissues.R.txt]]
<gallery width=800px height=800px>
<gallery widths=400px heights=400px>
File:GSI.22.tissues.png|Figure. Heatmap of normal tissues by high GSI regions.
File:GSI.22.tissues.png|Figure. Heatmap of normal tissues by high GSI regions.
</gallery>
</gallery>

Revision as of 04:29, 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


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)