[Genome] Table browser SNP vs genomic coordinates

[Brooke Rhead]

Hello Rob,

There is not an easy way around this using the Genome Browser.  As you 
have found, it is possible to format one coordinate region at a time 
using the "DNA" button and the extended case/color options, but it is 
not possible to format several regions at once, as the extended 
case/color options are not available in the Table Browser.  We have 
considered adding this functionality to the Table Browser, but it would 
be a computationally expensive, nontrivial feature to add there.

You may want to check the Galaxy website (http://main.g2.bx.psu.edu/) 
for a similar tool.  Galaxy is run by Penn State and works in 
conjunction with the Genome Browser.

One additional thing to be aware of: SNP insertions are not highlighted 
at all when using the extended case/color options.  See this discussion 
for more information:
http://www.soe.ucsc.edu/pipermail/genome/2006-August/011546.html

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Robert Osborne wrote:
> Hi,
> 
>  
> 
> I am trying to generate sequence data for a list of genomic coordinates with
> SNPs from the 126 table highlighted in bold or underlined.  
> 
>  
> 
> I can set up a custom track with a list of genomic coordinates and then
> download the sequence data for this track - but cannot figure out a way to
> get the SNP data highlighted onto the sequenced data.  If I type in
> individual coordinates into genome browser I can do this via the extended
> case/color options.  However, I can't do this in table browser and can't
> seem to find a way around this.  Can you help?
> 
>  
> 
> Best wishes,
> 
>  
> 
> Rob
> 
>  
> 
> Dr. Robert Osborne
> 
> Postdoctoral Research Associate to Nicola Ragge
> 
> Dept of Physiology, Anatomy and Genetics
> 
> Le Gros Clark Building
> 
> South Parks Rd
> 
> Oxford OX1 3QX
> 
>  
> 
> Office: 01865 282655
> 
> Lab: 01865 282834
> 
>  
> 
> _______________________________________________
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