Some of the bedtools (e.g., genomeCoverageBed,
complementBed, slopBed) need to know the size of the chromosomes for the
organism for which your BED files are based.

The way you do this for bedtools is to create a “genome” file, which simply lists the names of the chromosomes (or scaffolds, etc.) and their size (in basepairs).

Genome files must be tab-delimited and are structured as follows (this is an example for C. elegans):

chrI 15072421 chrII 15279323 ... chrX 17718854 chrM 13794

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