[Genome] ref_seq_id from bed coordinates

[Brooke Rhead]

Hello Pete,

To do this, first create a custom track of your genomic coordinates.  If 
you need more information on this step, the custom track user's guide is 
here: http://genome.ucsc.edu/goldenPath/help/customTrack.html.

Next, select the 'refGene' table in the Table Browser, then hit the 
"intersection: create" button.  Select your custom track as the table 
with which to intersect.  Choose one of the options under "These 
combinations will maintain the gene/alignment structure (if any) of 
RefSeq Genes" (otherwise, you will lose the refSeq ID information).  Hit 
"submit".

Now you can choose to output the lines from the refGene table that 
intersect with your custom track in whatever output format you wish to 
use (all fields, selected fields, BED, custom track, etc.).

Note that this method will return a list of the RefSeq Genes and their 
genomic coordinates.  The original genomic coordinates in the custom 
track you made will not be maintained.  If you need to keep information 
from both tables, there is another set of tools you could use, called 
"Galaxy", that works in conjunction with the UCSC Table Browser:

http://main.g2.bx.psu.edu/

Galaxy is run by Penn State.  Their helpdesk email is 
galaxy-user at bx.psu.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Pete Shepard wrote:
> Hello Browser Folks,
> 
> I have a list of genomic coordinates that map to regions in genes. Can you
> please tell me how I might use the Table Browser to get the refseq ids to
> which these coordinates map?
> 
> Thanks
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