liftover-coordinateslisted

# Convert Genomic Coordinates Between Assembly Versions ## When to Use - User needs to convert genomic coordinates between assemblies (hg19↔hg38, mm9↔mm10) - User asks about "liftover", "coordinate conversion", "assembly mismatch", or "CrossMap" - User has data in hg19/GRCh37 that needs conversion to GRCh38 (or vice versa) before integration - User wants to use UCSC liftOver or CrossMap for BED, VCF, bigWig, or BAM files - Example queries: "convert my hg19 peaks to hg38", "liftover coordinates for integration with ENCODE", "my data is in mm9, how do I convert to mm10?" Guide coordinate liftover between genome assemblies using UCSC liftOver, CrossMap, Ensembl REST API, and rtracklayer. Assembly conversion is one of the most common pitfalls in genomics — this skill provides the definitive workflow for safe, reproducible liftover with full provenance tracking. ## Scientific Rationale **The question**: "How do I safely convert my genomic coordinates from one assembly to another without losing data or introducing errors?" Assembly conversion is referenced as a critical step in 10+ other ENCODE Toolkit skills because ENCODE spans multiple data releases: some experiments were processed against hg19/GRCh37, while most current data uses GRCh38/hg38. Combining data across assemblies without proper liftover is one of the most common and most dangerous errors in computational genomics — coordinates that look valid in both assemblies may refer to completely different genomic locatio