Look up genomic regions in UCSC Browser
ucsc-browserskillsetup L2★35
ammawla/encode-toolkit ↗What it does
Query UCSC genome browser annotations and fetch genomic regions
Best for
Inspecting genomic regions when you need authoritative annotation without downloading entire genome builds.
Inputs
- · Genomic coordinates (chrom, start, end, assembly)
- · Annotation tracks (genes, repeats, conservation)
Outputs
- · Bed/GFF annotations for region
- · Conservation tracks
- · Repeats and regulatory elements
Requires
- · UCSC API / mysql interface
- · Genome assembly reference
- · Track definitions
Preconditions
Internet access to UCSC servers, valid genomic coordinates, knowledge of genome assembly versions
Failure modes
Invalid coordinates for assembly, track server down, assembly mismatch, coordinate system confusion (0-based vs 1-based)
Trust signals
- · Real-time UCSC data
- · Multi-track support
- · Cross-assembly coordinate conversion