Union Bed Graphs

union-bed-graphs

Quick Start

• Command: unionBedGraphs -i sample1.bg sample2.bg [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/unionBedGraphs
• Full reference: See references/help.md

When To Use This Tool

• Combine multiple bedGraph tracks into one interval-by-track matrix.
• Compare per-region coverage or signal values across replicates, conditions, or assays.
• Emit explicit empty intervals across a genome with -empty plus -g.
• Add headers and custom sample names for downstream plotting or statistics.

Common Patterns

# 1) Merge two bedGraph tracks onto shared intervals
unionBedGraphs \
  -i tumor.bg normal.bg \
  > tumor-normal.union.bg

# 2) Add a header with explicit sample names
unionBedGraphs \
  -i rep1.bg rep2.bg rep3.bg \
  -header \
  -names WT1 WT2 KO1 \
  > signal-matrix.tsv

# 3) Include empty genomic regions and use a custom missing-value filler
unionBedGraphs \
  -i sample1.bg sample2.bg \
  -g genome.sizes \
  -empty \
  -filler N/A \
  -header \
  > signal-with-gaps.tsv

Recommended Workflow

1. Ensure every input bedGraph is sorted by chromosome/start and contains non-overlapping intervals within each file.
2. Decide whether you want a plain numeric matrix, a labeled header via -header / -names, or explicit empty regions via -empty -g.
3. Choose the missing-value representation with -filler so downstream code does not confuse absent signal with a real zero unless that is intended.
4. Import the resulting unioned matrix into downstream QC, visualization, or statistical comparison workflows.

Guardrails

• -i is required and must be followed by one or more bedGraph files.
• Each input bedGraph must already be sorted by chrom,start and must not contain overlapping intervals within the same file.
• -empty requires -g so bedtools knows the chromosome extents.
• -names should provide one name per input file.
• Default filler text is 0; use -filler if a literal zero would be biologically misleading in your downstream analysis.
• Prefer -h or -examples for help; GNU-style --help and --version without -i only complain about missing input files.