Closest Bed

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

# 2) Report upstream/downstream signed distance relative to A strand
closestBed \
  -a peaks.bed \
  -b genes.bed \
  -D a \
  -io

# 3) Keep the two closest same-strand hits and break ties by file order
closestBed \
  -a exons.bed \
  -b transcripts.bed \
  -s \
  -k 2 \
  -t first

Recommended Workflow

1. Decide whether overlapping features should count as closest; if not, add -io.
2. Choose -d for absolute distance or -D ref|a|b if signed orientation matters biologically.
3. Apply -s / -S, -iu / -id, or -fu / -fd only after you are sure the strand and orientation model is the one you want.
4. Inspect cases with none / -1 output because they mean no candidate in B exists on the same chromosome.

Guardrails

• -iu, -id, -fu, and -fd require -D and inherit its upstream/downstream orientation rules.
• Ties are reported by default; if you need one record only, set -t first or -t last.
• With multiple B files, -mdb each and -mdb all produce meaningfully different semantics.
• Chromosome naming mismatches can make valid neighbors disappear silently into none / -1 results.
• Prefer -h for help; some --help / --version invocations on these wrappers produce extra errors.