bio-genome-intervals-bigwig-tracks
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bigwig-tracks --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bedtools 2.31+, numpy 1.26+, pandas 2.2+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # BigWig Tracks **"Read and create BigWig files"** → Access indexed binary signal tracks for efficient region queries and genome browser display. - Python: `pyBigWig.open('file.bw')` (pyBigWig) - CLI: `bigWigToBedGraph`, `bedGraphToBigWig` (UCSC tools) BigWig is an indexed binary format for continuous genomic data. Efficient for genome browsers and programmatic access. ## Why BigWig? | Format | Size | Random Access | Browser Support | |--------|------|---------------|-----------------| | bedGraph | Large | No | Limited | | bigWig | ~10x smaller | Yes (indexed) | Excellent | ## Convert bedGraph to bigWig (CLI) ### Installation ```bash # UCSC tools conda install -c bioconda ucsc-bedgraphtobigwig
- Version Compatibility
- Why BigWig?
- Convert bedGraph to bigWig (CLI)
- Installation
- Basic Conversion
- Get Chromosome Sizes
- Full Workflow
- Read BigWig with pyBigWig (Python)
- Open and Inspect
- Extract Values
- Binned Statistics
- Extract for BED Regions
- Create BigWig with pyBigWig
- deepTools for BigWig Operations
UCSC tools conda install -c bioconda ucsc-bedgraphtobigwig ucsc-bigwigtobedgraph Or download directly wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig chmod +x bedGraphToBigWig Sort bedGraph first (required) sort -k1,1 -k2,2n coverage.bedGraph > coverage.sorted.bedGraph Convert to bigWig bedGraphToBigWig coverage.sorted.bedGraph chrom.sizes output.bw chrom.sizes format: chr<TAB>size
What does the bio-genome-intervals-bigwig-tracks skill do?
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bigwig-tracks --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.