closest-bed

name	closest-bed
description	Use when you need to find the closest genomic feature in one file for each feature in another file, including distance calculations and strand-aware lookups.
disable-model-invocation	true
user-invocable	true

closest-bed

Quick Start

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

When To Use This Tool

• Find the nearest genomic feature in B for every feature in A.
• Report unsigned distance with -d or signed upstream/downstream distance with -D.
• Ignore overlaps and search only for nearby non-touching features with -io.
• Limit to same-strand or opposite-strand neighbors with -s / -S.
• Resolve ties or return multiple nearest hits with -t, -k, and -mdb.

Common Patterns

# 1) Find the nearest gene for each peak with distance
closestBed \
  -a peaks.bed \
  -b genes.bed \
  -d