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

Type

bash_script

License

MIT

Keywords

genomics

bedgraph

union

intervals

coverage

merge

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.bedgraph"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bedtools/bedtools_unionbedg/main.nf \  
  -params-file params.yaml

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

Name

Type & Properties

--files

-i

file

required

multiple

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'

Name

Type & Properties

--output

file

required

output

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

Name

Type & Properties

--header

boolean_true