fasta-from-bed

name	fasta-from-bed
description	Use when extracting DNA or RNA sequences from a FASTA file using coordinate ranges from BED, GFF, or VCF files.
disable-model-invocation	true
user-invocable	true

fasta-from-bed

Quick Start

• Command: fastaFromBed -fi reference.fa -bed intervals.bed [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/fastaFromBed
• Alias form: bedtools getfasta
• Full reference: See references/help.md

When To Use This Tool

• Extract sequence from a reference FASTA using interval coordinates.
• Retrieve exon, peak, promoter, or variant-adjacent sequences.
• Reverse-complement antisense features with -s.
• Concatenate BED12 blocks with -split.
• Emit FASTA, tabular, or BED-like sequence output depending on downstream needs.

Common Patterns

# 1) Basic sequence extraction to FASTA
fastaFromBed \
  -fi reference.fa \
  -bed peaks.bed \
  -fo peaks.fa

# 2) Strand-aware transcript sequence extraction
fastaFromBed \
  -fi reference.fa \
  -bed transcripts.bed \
  -s \
  -fo transcripts.fa

# 3) Extract concatenated BED12 block sequence in tabular form
fastaFromBed \
  -fi reference.fa \
  -bed transcripts.bed12 \
  -split \
  -tab > transcripts.tsv

Recommended Workflow

1. Make sure FASTA headers and interval chromosome names refer to the same assembly.
2. Choose the output mode deliberately: FASTA (default), -tab, or -bedOut.
3. Add -s for strand-aware extraction and -rna if the reference sequence alphabet is RNA.
4. Use -split only when BED12 block concatenation is the intended biology.

Guardrails

• -fi and -bed are required.
• Without -fo, output goes to stdout.
• -name+ is deprecated; prefer -name or -nameOnly.
• -split is for BED12 block extraction and changes the extracted sequence substantially.
• By default, strand is ignored; antisense features are only reverse-complemented when -s is set.