Visualizing microsats on a genome

msthoma · 06-15-2011, 02:07 AM

Hello everyone,

Does anybody know of a way that can be used to visually represent a large number of microsat markers in a genome? I have a large number of microsats (~20000) on the mouse genome, and I want to produce a figure showing a subset of them on the genome.

Thanks!

ulz_peter · 06-15-2011, 02:12 AM

If you just want to represent the microsatellite regions on the chromosome positions you could use the genome graph function of the UCSC Genome Browser:

http://genome.ucsc.edu/cgi-bin/hgGenome

you can upload a list of regions and it displays your data along the genome. Maybe that's what you're looking for...

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06-15-2011, 02:07 AM	#1
msthoma Junior Member Location: Montpellier Join Date: Jun 2011 Posts: 1	Visualizing microsats on a genome Hello everyone, Does anybody know of a way that can be used to visually represent a large number of microsat markers in a genome? I have a large number of microsats (~20000) on the mouse genome, and I want to produce a figure showing a subset of them on the genome. Thanks!

06-15-2011, 02:12 AM	#2
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	If you just want to represent the microsatellite regions on the chromosome positions you could use the genome graph function of the UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgGenome you can upload a list of regions and it displays your data along the genome. Maybe that's what you're looking for...