bedtools/bedtools_reldist
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
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 |
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 |
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 |
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 v0.4.2 \
-main-script target/nextflow/bedtools/bedtools_reldist/main.nf \
-params-file params.yaml Relationships
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