TCGA WGBS, PMD and Solo-WCGW CpGs

Annotation data from Zhou, Dinh et al. Nature Genetics 2018

Solo-WCGW CpGs and PMD Definitions

Human hg19

  • Coordinates of Solo-WCGW CpGs Genomewide
  • Coordinates of Solo-WCGW CpGs in common PMDs
  • Coordinates of PMDs/HMDs and common PMDs/HMDs
  • View Annotation in UCSC Genome Browser.

Human hg38

  • Coordinates of Solo-WCGW CpGs Genomewide
  • Coordinates of Solo-WCGW CpGs in common PMDs
  • Coordinates of PMDs/HMDs and common PMDs/HMDs
  • View Annotation in UCSC Genome Browser.

Mouse mm10

  • Coordinates of Solo-WCGW CpGs Genomewide
  • Coordinates of Solo-WCGW in common PMDs
  • Coordinates of PMDs/HMDs and common PMDs/HMDs
  • View Annotation in UCSC Genome Browser.

Mouse mm39

  • Coordinates of Solo-WCGW CpGs Genomewide

Infinium HumanMethylation BeadChip

TCGA Cancer Methylomes

Human hg19

  • Methylomes in UCSC Genome Browser
  • Methylation Bed Files (4th column: methylation level; 5th column: sequencing depth; 6th column: C and G before merging)
Note: a known naming typo/mismatch: COAD_3158/COAD_N3158 should be COAD_3518/COAD_N3518

Human hg38

  • Methylomes in UCSC Genome Browser
  • Methylation Bed Files (4th column: methylation level; 5th column: sequencing depth)
  • MultiQC Reports (BISCUIT, FastQC etc).
Methylation in YAME MU format hg38 — 47 samples, all CpGs with depth ≥ 1 doi:10.5281/zenodo.23217816
Coordinates: yame fetch hg38/cpg_nocontig.cr. Example (M and U per CpG):
yame subset 20260708_TCGA_WGBS.cg TCGA_BLCA_A1AG | yame unpack -f -1 -
See YAME. COAD samples are named COAD_3518/COAD_N3518 here.
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