bedtools getfasta 提取某区域fasta文件

帮助文档

Version: v2.28.0
Summary: Extract DNA sequences from a fasta file based on feature coordinates.

Usage:   bedtools getfasta [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>

Options: 
    -fi Input FASTA file
    -fo Output file (opt., default is STDOUT
    -bed    BED/GFF/VCF file of ranges to extract from -fi
    -name   Use the name field for the FASTA header
    -name+  Use the name field and coordinates for the FASTA header
    -split  given BED12 fmt., extract and concatenate the sequences
        from the BED "blocks" (e.g., exons)
    -tab    Write output in TAB delimited format.
        - Default is FASTA format.

    -s  Force strandedness. If the feature occupies the antisense,
        strand, the sequence will be reverse complemented.
        - By default, strand information is ignored.

    -fullHeader Use full fasta header.
        - By default, only the word before the first space or tab 
        is used.

getfasta

$ bedtools getfasta -fi /teach/database/reference/hg38.fa -bed access.hg38.bed.10k >hg38.10k.bed.fa

$ bedtools getfasta -fi /teach/database/reference/hg38.fa -bed access.hg38.bed.10k -fo hg38.10k.bed.fa

其他命令可以自行测试。