BEDtools.md
Update: 2025.6.2Reference: BEDtools GitHub
1. BEDtools Intersect
The bedtools intersect
command identifies overlapping features between two files.
Examples:
# Find overlaps between RefSeq exons (RefSeq.gtf) and Alu annotations (Alus.bed)
bedtools intersect -a RefSeq.gtf -b Alus.bed -wo
# Treat each block in BED12 format as a separate interval
bedtools intersect -a RefSeq.bed -b Alus.bed -wo -split
# Include all features, even those with no overlaps
bedtools intersect -a RefSeq.bed -b Alus.bed -wao
2. BAM to BED Conversion
The bedtools bamtobed
command converts BAM files to BED format.
Examples:
# Convert BAM to BED and add the CIGAR string as the seventh column
bedtools bamtobed -i sample.bam -cigar > sample.bed
# Use the `-split` option to split spliced alignments into individual exon blocks
bedtools bamtobed -i sample.bam -split > sample_split.bed
3. BED to BAM Conversion
The bedtools bedtobam
command converts BED files to BAM format.
Examples:
# Convert BED to BAM using a genome header file (contains chromosome lengths)
bedtools bedtobam -i sample.bed -g genome_header.txt > sample.bam
# Use the `-bed12` option to preserve exon blocks in BED and write CIGAR strings to BAM
bedtools bedtobam -i sample.bed -g genome_header.txt -bed12 > sample_exon.bam
4. Extracting FASTA Sequences from BED Regions
The bedtools getfasta
command extracts FASTA sequences for specified regions in a BED file.
Examples:
# Extract FASTA sequences for regions specified in a BED file
bedtools getfasta -fi genome.fa -bed regions.bed -fo output.fasta
# Use the `-split` option to extract and merge exon regions
bedtools getfasta -fi genome.fa -bed exons.bed -fo exons_output.fasta -split
This cheatsheet provides concise usage examples for common BEDtools commands, making it an essential reference for bioinformatics workflows. For detailed documentation, visit the official BEDtools documentation.
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