cyberneticlibrary
← library

Aggregate DNA methylation maps across samples

methylation-aggregationskillsetup L3★35
ammawla/encode-toolkit ↗
What it does

Build tissue-level DNA methylation maps by aggregating WGBS per-CpG data across experiments

Best for

Understanding tissue-specific regulatory chromatin state when aggregated epigenetic methylation landscape is the bottleneck.

Inputs
  • · ENCODE WGBS experiment accessions
  • · Tissue of interest
  • · Assembly (GRCh38)
Outputs
  • · Per-CpG averaged methylation levels
  • · HMR/PMD region calls
  • · Tissue-specific methylation landscape
Requires
  • · ENCODE/UCSC genomics APIs
  • · HTTP/REST API
  • · Git/GitHub
Preconditions
  • · ENCODE API access
  • · Bisulfite conversion >=98%
  • · Mean CpG coverage >=10x
Failure modes
  • · Low-coverage CpGs have inflated variance
  • · Cross-lab batch effects shift methylation baselines
  • · HMR calling is assembly-specific
Trust signals
  • · Cites Roadmap Epigenomics (aggregation protocol)
  • · ENCODE Phase 3 integration patterns
  • · Quality gates per experiment