map-bed

name	map-bed
description	Use when you need to apply aggregation functions (sum, mean, count, etc.) to values from overlapping intervals in one file and map them onto intervals from another file.
disable-model-invocation	true
user-invocable	true

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