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Old 02-17-2012, 03:57 PM   #1
Ooinp
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Default Chromosome start and end coordinates

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.
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Old 04-23-2012, 11:13 AM   #2
dariober
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Quote:
Originally Posted by Ooinp View Post
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)
Code:
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
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