Random Bed

random-bed

Quick Start

• Command: randomBed -g genome.txt [-l length] [-n count] [-seed int]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/randomBed
• Full reference: See references/help.md

When To Use This Tool

• Generate simple random genomic intervals from a genome definition.
• Build background interval sets for simulations or quick null distributions.
• Produce many fixed-length windows without reference to an input BED file.
• Create reproducible random sets with -seed.

Common Patterns

# 1) Generate 10,000 random 500 bp intervals
randomBed \
  -g genome.txt \
  -l 500 \
  -n 10000 > random.bed

# 2) Reproducible random intervals
randomBed \
  -g genome.txt \
  -l 1000 \
  -n 5000 \
  -seed 42 > random.seed42.bed

# 3) Use a FASTA index as genome source
randomBed \
  -g reference.fa.fai \
  -l 200 \
  -n 1000

Recommended Workflow

1. Build a valid genome file first, typically from a FASTA .fai.
2. Set interval length and count explicitly rather than relying on defaults.
3. Add -seed for reproducibility if the output will be reused or published.
4. Filter or post-process the output afterward if you need exclusion masks, chromosome preservation, or non-overlap constraints.

Guardrails

• -g is required.
• Defaults are surprisingly large: 100 bp intervals and 1,000,000 records.
• randomBed is unconstrained random generation; if you need exclusion masks or same-chromosome shuffling of an existing BED set, use shuffleBed instead.
• The genome file is tab-delimited chromosome name plus size; a FASTA .fai works because bedtools reads only the first two columns.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.