liftover-coordinates
CommunityReliable genomic coordinate conversion between assemblies.
Authorammawla
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill enables accurate conversion of genomic coordinates between different genome assemblies, preventing errors in data integration.
Core Features & Use Cases
- Coordinate Liftover: Guides users through transforming coordinates between assemblies like hg19 and hg38, or mm9 and mm10, using tools like UCSC liftOver, CrossMap, or Ensembl API.
- Provenance Tracking: Logs conversion details including chain files, tools, and loss rates to ensure reproducibility.
- Use Case: A researcher wants to combine GWAS data from hg19 with ENCODE peaks aligned to GRCh38. This Skill automates the liftover process, handles unmapped regions, and records the operation for reproducibility.
Quick Start
Input the coordinates in the source assembly and specify target assembly; then run the liftover process for accurate position mapping.
Dependency Matrix
Required Modules
CrossMapUCSC chain filesEnsembl REST APIrtracklayer
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: liftover-coordinates Download link: https://github.com/ammawla/encode-toolkit/archive/main.zip#liftover-coordinates Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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