Chromosome start and end coordinates

[Ooinp]

This should be easy in theory, but is driving me desperate: I need chromosome start and end coordinates for hg19, hg18 including pseudoautosomal regions. Would be nice if there is a simple way to get the same for mouse, rat, zebrafish but this is luxury.

[dariober]

This should be easy in theory, but is driving me desperate: I need chromosome start and end coordinates for hg19, hg18 including pseudoautosomal regions. Would be nice if there is a simple way to get the same for mouse, rat, zebrafish but this is luxury.

Start and end coordinates can be accessed via MySQL with something like:
(change species/build as appropriate)

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

Or from ftp://hgdownload.cse.ucsc.edu/golden...romInfo.txt.gz

Not sure where pseudoautosomal region are stored but you can see them in the Assembly Detail paragraph at http://genome.ucsc.edu/cgi-bin/hgGateway

Hope this helps

Dario