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bio-genome-intervals-bed-file-basics

Maintainer FreedomIntelligence · Last updated April 1, 2026

Read, write, and filter BED files with pybedtools/bedtools.

OpenClawNanoClawAnalysisReproductionbio-genome-intervals-bed-file-basics🧠 bioos extended suitebioos extended bioinformatics suiteread

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-intervals-bed-file-basics

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

BED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.
echo -e "chr1\t100\t200\nchr1\t300\t400" > regions.bed.

Source Doc

Excerpt From SKILL.md

Coordinate System

BED uses 0-based, half-open coordinates:

Start: 0-based (first base is 0)
End: exclusive (not included)
Position 100-200 means bases at positions 100-199

Create BED6 with name and strand

echo -e "chr1\t100\t200\tpeak1\t100\t+" > peaks.bed


## From string

bed_string = '''chr1\t100\t200\tpeak1\t100\t+
chr1\t300\t400\tpeak2\t200\t-'''
bed = pybedtools.BedTool(bed_string, from_string=True)

Use cases

Use bio-genome-intervals-bed-file-basics for genomics and bioinformatics workflows.
Apply bio-genome-intervals-bed-file-basics to sequencing, variant, or omics analysis tasks.