bio-bedgraph-handling
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bedgraph-handling --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+, 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. # bedGraph Handling **"Work with bedGraph signal tracks"** → Create, manipulate, and convert bedGraph files for displaying coverage or signal intensity on genome browsers. - CLI: `bedtools genomecov -bg` to generate, `bedGraphToBigWig` to convert - Python: `pyBigWig`, `pybedtools` bedGraph is a text format for displaying continuous-valued data on genome browsers. Common for coverage, signal intensity, and scores. ## bedGraph Format ``` track type=bedGraph name="Sample" description="Coverage" chr1 0 100 1.5 chr1 100 200 2.3 chr1 200 300 0.8 ``` Four columns: chrom, start, end, value (0-based, half-open) ## Create bedGraph from BAM ### Using bedtools genomecov ```bash bedtools genomecov -ibam sample.bam -bg > sample.bedg
- Version Compatibility
- bedGraph Format
- Create bedGraph from BAM
- Using bedtools genomecov
- Strand-Specific
- 5' End Coverage (ChIP-seq)
- Normalize by Library Size (CPM)
- Sort bedGraph
- Convert bedGraph to bigWig
- Using UCSC bedGraphToBigWig
- Generate chrom.sizes
- Clip to Chromosome Boundaries
- Convert bigWig to bedGraph
- Merge bedGraph Files
bedtools genomecov -ibam sample.bam -bg > sample.bedgraph bedtools genomecov -ibam sample.bam -bg -split > sample.bedgraph bedtools genomecov -ibam sample.bam -bg -scale 1.5 > sample.scaled.bedgraph bedtools genomecov -ibam sample.bam -bg -strand + > sample.plus.bedgraph bedtools genomecov -ibam sample.bam -bg -strand - > sample.minus.bedgraph bedtools genomecov -ibam sample.bam -bg -5 > sample.5prime.bedgraph bedtools genomecov -ibam sample.bam -bg -scale $scale > sample.cpm.bedgraph sort -k1,1 -k2,2n sample.bedgraph > sample.sorted.bedgraph bedGraphToBigWig sample.sorted.bedgraph chrom.sizes sample.bw fetchChromSizes hg38 > hg38.chrom.sizes
What does the bio-bedgraph-handling skill do?
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bedgraph-handling --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.