ucsc-browserlisted

# Query the UCSC Genome Browser REST API ## When to Use - User wants to query the UCSC Genome Browser REST API for tracks, sequences, or cCRE annotations - User asks about "UCSC", "genome browser", "cCREs", "track hub", or "sequence retrieval" - User needs to retrieve DNA sequences for peak regions or regulatory elements - User wants to intersect ENCODE peaks with UCSC-hosted annotations (cCREs, conservation, repeat masker) - Example queries: "get cCRE annotations for my region", "fetch DNA sequence under my peaks", "query UCSC for conservation scores at my enhancers" Retrieve regulatory annotations, DNA sequences, TF binding data, and ENCODE-hosted tracks from the UCSC Genome Browser programmatic interface. ## Scientific Rationale **The question**: "What regulatory annotations exist at this genomic locus, and what is the underlying sequence?" The UCSC Genome Browser hosts the most comprehensive collection of genome annotations, including ENCODE cCREs (926,535 human), TF rPeak clusters (21.8M from 912 factors across 1,152 biosamples), DNase clusters, conservation scores, and gene models. The REST API at `api.genome.ucsc.edu` enables programmatic access without authentication. ### Why UCSC Complements the ENCODE Portal The ENCODE Portal (`encodeproject.org`) provides experiment-level data — individual ChIP-seq peaks, BAM files, quality metrics. UCSC provides **aggregated, cross-experiment annotations**: which cCREs overlap your region, which TFs bind there across all E