Window Bed

# 2) Query a strand-aware promoter window: 2 kb upstream, 500 bp downstream
windowBed \
  -a transcripts.bed \
  -b atac-peaks.bed \
  -l 2000 \
  -r 500 \
  -sw \
  -sm

# 3) Count nearby features instead of returning paired records
windowBed \
  -a genes.bed \
  -b enhancers.bed \
  -w 100000 \
  -c

Recommended Workflow

1. Decide whether you need the default paired-output join, a presence/absence view (-u, -v), or counts (-c).
2. Choose a symmetric window with -w or an asymmetric design with -l and -r.
3. Add -sw only when upstream/downstream should be interpreted relative to strand, and add -sm or -Sm only when overlap partners must match or oppose strand.
4. If A is BAM, switch to -abam and choose whether output should stay BAM-like or be converted with -bed.

Guardrails

• -a and -b are both required unless BAM input is supplied through -abam, which replaces -a.
• If you do not specify -w, -l, or -r, bedtools uses a default symmetric window of 1000 bp.
• Default output emits the full A and full B record for every hit; -u, -c, and -v change the row count and layout substantially.
• -sw changes how left/right windows are interpreted relative to feature strand; it is different from -sm / -Sm, which filter the strand relationship between A and B.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.