bedtools/bedtools_unionbedg
genomics
bedgraph
union
intervals
coverage
merge
Description
Combine multiple BEDGRAPH files into a single file reporting the union of all intervals.
bedtools unionbedg combines multiple BEDGRAPH files into a single file, reporting the union
of all intervals and their values across files. For each genomic position, it reports the
values from each input file, using '0' for positions not covered in a particular file.
This tool is commonly used for:
Combining coverage tracks from multiple samples
Creating unified coverage matrices for comparative analysis
Merging signal tracks for visualization
Preparing data for multi-sample analysis workflows
Inputs
Name | Type & Properties | Description |
|---|---|---|
--files -i | file required multiple | Input BEDGRAPH files to combine into a union. **Format:** BEDGRAPH files with chromosome, start, end, and value columns **Content:** Genomic intervals with associated numeric values (coverage, scores, etc.) **Usage:** All intervals from all files will be combined into a unified output **Requirements:** Files should use consistent chromosome naming **Output:** Union of all intervals with values from each input file |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output file containing the union of all input BEDGRAPH intervals. **Format:** BEDGRAPH format with additional value columns for each input file **Content:** Union of intervals with values from all input files **Columns:** Chromosome, start, end, followed by one value column per input file **Missing values:** Positions not covered in a file are represented as '0' |
Options
Name | Type & Properties | Description |
|---|---|---|
--header | boolean_true | Write header line with input file names to the output. **Usage:** Adds a header line showing the source of each value column **Format:** Header contains input filenames corresponding to value columns **Default:** false (no header written) **Applications:** Useful for tracking which column corresponds to which input file |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.bedgraph"
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_unionbedg/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_unionbedgbiobox v0.4.2
Uses
0 relationships
No component dependencies found.