AG
Data & Repro
agent-browser
Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…
FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-genome-intervals-coverage-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
Compute read depth coverage across genomic regions.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-intervals-coverage-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Calculate coverage and depth across genomic regions using bedtools and pybedtools.
- bedtools genomecov -ibam alignments.bam -bg > coverage.bedGraph.
Source Doc
Excerpt From SKILL.md
Include zero-coverage regions
bedtools genomecov -ibam alignments.bam -bga > coverage_with_zeros.bedGraph
Split by strand
bedtools genomecov -ibam alignments.bam -bg -strand + > plus_strand.bedGraph bedtools genomecov -ibam alignments.bam -bg -strand - > minus_strand.bedGraph
Scale by total reads (RPM normalization)
TOTAL=$(samtools view -c alignments.bam) SCALE=$(echo "scale=10; 1000000/$TOTAL" | bc) bedtools genomecov -ibam alignments.bam -bg -scale $SCALE > normalized.bedGraph
Use cases
- Use bio-genome-intervals-coverage-analysis for genomics and bioinformatics workflows.
- Apply bio-genome-intervals-coverage-analysis to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- bigwig-tracks - Convert bedGraph to bigWig
- alignment-files/sam-bam-basics - BAM processing
- interval-arithmetic - Intersect with regions
- chip-seq/chipseq-visualization - Peak coverage analysis
Related skills
Related skills
AL
Data & Repro
alpha-vantage
Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators.
K-Dense-AI/claude-scientific-skillsView
BI
Data & Repro
bio-alignment-filtering
Filter alignments by flag, quality, region, or paired status.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-alignment-indexing
Index BAM/CRAM files with samtools index for random access.
FreedomIntelligence/OpenClaw-Medical-SkillsView