npm

bedtools

Tools for genome arithmetic and set theory operations on genomic intervals

brewmacoslinux
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About

Tools for genome arithmetic (set theory on the genome)

Commands

bedtoolsintersectBedmergeBedcoverageBedfastaFromBedbamToBedbedToIgv

Examples

Find overlapping intervals between two BED files$ bedtools intersect -a file1.bed -b file2.bed
Merge overlapping BED intervals$ bedtools merge -i sorted_file.bed
Extract FASTA sequences from genomic coordinates$ bedtools getfasta -fi reference.fa -bed regions.bed -fo output.fa