Hi, getting the lenght of each chromosome of your reference genome (or fasta file), you can use bedtools makewindows to divide it in regions and represent them in bed format.

For example, to divide the human genome into windows of 1MB:

$ bedtools makewindows -g hg19.txt -w 1000000 > hg19_1Mb.bed

where hg19.txt, the file containing chromosome lengths, has the following tab delimited format:

chr1    249250621
chr2    243199373
...