Nuc Bed

# 2) Strand-aware sequence composition with extracted sequence
nucBed \
  -fi reference.fa \
  -bed transcripts.bed \
  -s \
  -seq

# 3) Count motif occurrences inside intervals
nucBed \
  -fi reference.fa \
  -bed peaks.bed \
  -pattern CG \
  -C

Recommended Workflow

1. Ensure FASTA headers and interval chromosome names refer to the same coordinate system.
2. Start with the default composition output before adding sequence extraction or motif counting.
3. Add -s only when the strand of the intervals matters for interpretation.
4. Validate a few rows manually when motif counts or sequence extraction drive downstream conclusions.

Guardrails

• -fi and -bed are both required.
• -pattern is case-sensitive unless -C is added.
• -fullHeader changes FASTA header matching behavior; use it only if the interval identifiers depend on full deflines rather than the first token.
• -seq increases output width substantially by appending extracted sequence text.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.