Shift Bed

# 2) Shift plus and minus strands in opposite directions
shiftBed \
  -i transcripts.bed \
  -g genome.sizes \
  -p 500 \
  -m -500

# 3) Shift by 10% of each feature length
shiftBed \
  -i intervals.bed \
  -g genome.sizes \
  -s 0.10 \
  -pct

Recommended Workflow

1. Prepare a genome file (or FASTA .fai) so bedtools can clamp shifted features to chromosome bounds.
2. Decide whether the shift is uniform with -s or strand-specific with -p and -m.
3. Decide whether values are absolute base pairs or fractions of feature length via -pct.
4. Inspect the output for boundary clipping at chromosome starts and ends before using it in downstream analysis.

Guardrails

• -i and -g are both required.
• Use either -s alone or -p together with -m; those modes are mutually exclusive.
• With -pct, values like 0.10 mean 10% of feature length, not 0.10 bp.
• Starts are clipped to 0 and ends are clipped to chromosome length when a shift would move a feature out of bounds.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.