ucsc-genome-browser-querier

name	ucsc-genome-browser-querier
description	UCSC Genome Browser query skill for genome annotation retrieval and track data access
allowed-tools	["Read","Write","Glob","Grep","Edit","WebFetch","WebSearch","Bash"]
metadata	{"version":"1.0","category":"bioinformatics","tags":["infrastructure","annotation","ucsc","tracks"]}
graph	{"domains":["domain:bioinformatics"],"specializations":["specialization:biomedical-informatics"],"skillAreas":["skill-area:data-analysis","skill-area:python-data-pipelines","skill-area:graph-algorithms"],"workflows":["workflow:experiment-design"],"roles":["role:research-engineer","role:biomedical-engineer"]}

UCSC Genome Browser Querier Skill

Purpose

Provide UCSC Genome Browser queries for genome annotation retrieval and track data access.

Capabilities

• Track data retrieval
• Custom track upload
• Genome annotation queries
• Conservation score extraction
• Table browser queries
• bigWig/bigBed handling

Usage Guidelines

• Query relevant annotation tracks
• Upload custom data for visualization
• Extract conservation scores for analysis
• Use Table Browser for data extraction
• Handle bigWig/bigBed formats efficiently
• Document genome assembly versions

Dependencies

• UCSC API
• kent utilities
• pyBigWig

Process Integration

• Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
• RNA-seq Differential Expression Analysis (rnaseq-differential-expression)