BedTools can't find "hg19.genome"

Question

[biostart]

Hello,

I am running the following command:

bedtools random -n 100000 -l 118 -g hg19.genome >random_h19.bed

and get this error:

Error: The requested genome file (hg19.genome) could not be opened. Exiting!

Any ides how to specify the path to "hg19.genome" and where to find it? (We have an old version of bedtools installed on a large cluster).

Thanks!

Answer 1

[GenoMax]

It is a file with the chromosome sizes: https://github.com/arq5x/bedtools/blob/master/genomes/human.hg19.genome

[biostart]

Ok, I downloaded the genome file from the UCSC web site and manually put it in my folder, now it works

[cheyujlee]

Yes, above comment by @biostart works.