Ns126:Calendar/NOTES/2015-8-31

From ZhangLabWiki
Revision as of 04:09, 23 September 2015 by >Shicheng
Jump to navigation Jump to search


  • 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
ID Type
Colon-primary-tumor Tumor
HCT116 Tumor
WB-centenarian WB
WB-middle-age WB
WB-new-born WB
STL002AO-01 Vessel
STL003AO-01 Vessel
STL001TH-01 Thymus
N37-Stomach Stomach
STL002GA-01 Stomach
STL001SX-01 Spleen
STL002SX-01 Spleen
STL003SX-01 Spleen
STL002PA-01 Pancreas
N37-Pancreas Pancreas
STL003PA-01 Pancreas
STL002OV-01 Ovary
N37-SM muscle
STL001PO-01 muscle
STL002PO-01 muscle
STL003PO-01 muscle
N37-Lung Lung
STL001LG-01 Lung
STL002LG-01 Lung
N37-Liver Liver
STL011LI-01 Liver
STL002AD-01 Kidney
STL003AD-01 Kidney
N37-SI Intestine
STL001SB-01 Intestine
STL002SB-01 Intestine
STL003SB-01 Intestine
N37-Heart Heart
STL001LV-01 Heart
STL001RV-01 Heart
STL003LV-01 Heart
STL003RA-01 Heart
STL003RV-01 Heart
methylC-seq-h1+bmp4-r1 H1
methylC-seq-h1+bmp4-r2 H1
methylC-seq-h1-mesendoderm-r1 H1
methylC-seq-h1-mesendoderm-r2 H1
methylC-seq-h1-msc-r1 H1
methylC-seq-h1-msc-r2 H1
methylC-seq-h1-npc-r1 H1
methylC-seq-h1-npc-r2 H1
methylC-seq-h1-r1 H1
methylC-seq-h1-r2 H1
STL001GA-01 Gastric
STL003GA-01 Gastric
STL001FT-01 Fat cell
STL002FT-01 Fat cell
STL003FT-01 Fat cell
STL002EG-01 Esophagus
STL003EG-01 Esophagus
N37-Colon Colon
STL001SG-01 Colon
STL003SG-01 Colon
N37-CRBL Brain
N37-FL Brain
STL001BL-01 Bladder

File:GSI.22.tissues.png File:Code.20190903.TSI.22.tissues.R.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 discuss with Dinh, the methylFreq files of 106 samples were collected (10 N37, 36 Salk, 57 MONOD and 3 Heyn2013Age)