bedtools/bedtools_reldist

genomics

distance

distribution

spatial-analysis

clustering

statistics

colocalization

Description

Calculate the relative distance distribution between two feature files.

bedtools reldist computes the distribution of relative distances between features
in two genomic datasets. This tool is useful for understanding spatial relationships
and clustering patterns between different types of genomic features.

The tool calculates relative distances by measuring how close features in dataset A
are to the nearest features in dataset B, normalized by the distance between adjacent
features in dataset B. This provides insights into whether features cluster together
more than expected by chance.

This tool is commonly used for:

Analyzing spatial clustering of genomic features
Comparing distributions of regulatory elements
Quality control of feature calling algorithms
Statistical analysis of genomic co-localization
Studying relationships between different genomic annotations
Identifying non-random spatial patterns in genomic data

Type

bash_script

License

MIT

Keywords

genomics

distance

distribution

spatial-analysis

clustering

statistics

colocalization

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.txt"  
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_reldist/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--bed_a -a	file required	First input BED/GFF/VCF file with genomic features. Format: BED, GFF, or VCF file with genomic coordinates Content: Primary feature set for distance calculation Usage: Distances will be calculated FROM these features TO features in dataset B Requirements: Standard genomic coordinate format
--bed_b -b	file required	Second input BED/GFF/VCF file with genomic features. Format: BED, GFF, or VCF file with genomic coordinates Content: Reference feature set for distance calculation Usage: Distances will be calculated TO these features FROM features in dataset A Requirements: Standard genomic coordinate format

Name

Type & Properties

--bed_a

-a

file

required

--bed_b

-b

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with relative distance analysis results. Format: Tab-delimited text file Content: Either summary statistics or detailed per-interval distances Summary mode: Distribution bins and frequencies Detail mode: Individual relative distances for each interval in dataset A

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--detail	boolean_true	Report the relative distance for each interval in dataset A. Default: Summary mode (distribution statistics) Detail mode: Individual relative distance for each feature in A Usage: Provides granular distance information for downstream analysis Output: One line per feature in dataset A with its relative distance

Name

Type & Properties

--detail

boolean_true