bedtools/bedtools_random

genomics

random

intervals

simulation

control

sampling

null-dataset

Description

Generate random intervals among a genome.

bedtools random generates a specified number of random intervals with a defined length
across a reference genome. This tool is useful for creating random genomic regions for
statistical analysis, generating null datasets for enrichment testing, or creating
control datasets for comparative genomics studies.

This tool is commonly used for:

Creating random control regions for enrichment analysis
Generating null datasets for statistical testing
Producing background intervals for comparative studies
Creating random sampling of genomic space
Building control datasets for machine learning applications
Testing genomic analysis pipelines with known random data

Type

bash_script

License

MIT

Keywords

genomics

random

intervals

simulation

control

sampling

null-dataset

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bed"  
length: [ 100 ]  
number: [ 1000000 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/bedtools/bedtools_random/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--genome -g	file required	Genome file with chromosome names and sizes. Format: Tab-delimited file with chromosome information Content: Each line contains: <chromName><TAB><chromSize> Requirements: Chromosome names and their corresponding sizes in base pairs Creation: Can be generated using `samtools faidx` on FASTA files Example: chr1<TAB>249250621

Name

Type & Properties

--genome

-g

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with generated random intervals. Format: 6-column format (chrom, start, end, name, score, strand) Content: Randomly placed intervals across the specified genome Coordinates: 0-based start, 1-based end (standard BED format) Additional columns: Sequential name, score (interval length), random strand Ordering: Intervals are not necessarily sorted by position

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--length -l	integer	Length of the intervals to generate in base pairs. Default: 100 Usage: All generated intervals will have this fixed length Range: Positive integer values Considerations: Length should be reasonable relative to chromosome sizes
--number -n	integer	Number of intervals to generate. Default: 1,000,000 Usage: Total number of random intervals to create Range: Positive integer values Considerations: Large numbers may take longer to generate and require more memory
--seed	integer	Integer seed for random number generation. Default: Automatically chosen seed (non-deterministic) Usage: Provides reproducible results when the same seed is used Range: Any integer value Applications: Essential for reproducible analyses and testing

Name

Type & Properties

--length

-l

integer

--number

-n

integer

--seed

integer