Map Bed

map-bed

Quick Start

• Command: mapBed -a A.bed -b B.bed -c <B_col> -o <op> [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/mapBed
• Full reference: See references/help.md

When To Use This Tool

• Aggregate values from overlapping B intervals onto each A interval.
• Summarize signal tracks, counts, names, or scores across target intervals.
• Attach mean, sum, min, max, count, or distinct summaries to an interval set.
• Constrain which overlaps contribute with strand or reciprocal-overlap rules.

Common Patterns

# 1) Mean signal from B column 5 over each A interval
mapBed \
  -a exons.bed \
  -b signal.bed \
  -c 5 \
  -o mean

# 2) Count distinct overlapping labels
mapBed \
  -a peaks.bed \
  -b annotations.bed \
  -c 4 \
  -o count_distinct

# 3) Map multiple B columns with matching operations
mapBed \
  -a peaks.bed \
  -b signal.bed \
  -c 4,5 \
  -o distinct,mean

Recommended Workflow

1. Sort both files by chromosome and start coordinate before running mapBed.
2. Decide which B columns carry the statistic you actually want to summarize.
3. Choose aggregation operators that match the column type: numeric ops for numeric columns, collapse / distinct for labels.
4. Add -s, -S, -f, -F, -r, or -e only if overlap eligibility needs to be biologically constrained.

Guardrails

• Both inputs must be sorted by chromosome then start.
• -c refers to columns in B, not A.
• If you provide multiple -c columns and multiple -o operators, the counts must align unless you intentionally rely on the single-column / single-op broadcast behavior.
• collapse keeps duplicates whereas distinct removes them.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.