Custom Genome Size - marcrusso/DROPA GitHub Wiki

As reported in main page, Bedtools shuffle requires a genome size file containing a listof all chromosome and their dimension. It is structured as follow:

<ChromosomeName><TAB><ChromosomeSize>

If you created a new Gene Reference from UCSC Table Browser, you can download a new genome size with this command (substitute hg19 with your genome version):

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg19.chromInfo" > hg19.genome