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Old 08-01-2010, 01:36 PM   #1
dafil
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Location: canada

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Default Need Help On NCBI ref Gene coordinates File

Hi,
I am a bit new about browsing genome . In my study, i require a flat file containing UCSC hg18 ref known gene coordinates for the forward strand.
i.e. example
chr start end geneName
chr1 1000 2000 geneX

I have tried and browsed ucsc but couldn't figure out a way to produce a flat file with these info. Can anyone please help me on this .
thanks.
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Old 08-01-2010, 05:15 PM   #2
adamdeluca
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Use the table browser, select your favorite gene table (refFlat etc.), select BED as the output format.

http://genome.ucsc.edu/cgi-bin/hgTab...a_doMainPage=1
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Old 08-02-2010, 12:49 PM   #3
dafil
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thanks a lot.
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Old 02-10-2011, 01:53 AM   #4
jsp
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Default Need Help On NCBI ref Gene coordinates File

Hi,

I need the geneName to be CBFB, SOX2, etc, which group/track should I choose?
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Old 02-10-2011, 02:49 AM   #5
shruti
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Change the track to RefSeq Genes.
Download the primary info format. You can choose to remove the info u don't want.

Last edited by shruti; 02-10-2011 at 03:00 AM.
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Old 02-10-2011, 03:57 AM   #6
jsp
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shruti, thanks a lot.
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