[Genome] Question on the exon structure

[Galt Barber]

Hi, Jin

We think you may be able to do this with a BED 9 custom track.
You can give each set a different color.  All probes in the
same set will share the same color.

 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED

I haven't actually seen your probe data, so this is just an example.
You would probably set fields as follows:
 chrom       (col 1) e.g. chr22
 chromStart  (col 2) e.g. 20001
 chromEnd    (col 3) e.g. 20200
 name        (col 4) e.g. coolProbeId999
 score       (col 5) just set to 0 if unneeded
 strand      (col 6) just set to + if unneeded
 thickStart  (col 7 = col 2) set to chromStart
 thickEnd    (col 8 = col 3) set to chromEnd
 itemRgb     (col 9 = r,g,b) where r,g,b are range 0 to 255.
           e.g. 255,0,255 = red and blue = purple

You need to set the custom track line attribute itemRgb=On.

 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks

This should allow you to color your sets.
The system will probably work better if you can
stick to fewer than 10 different colors.

-Galt


On Fri, 1 Feb 2008, Ma, Jin wrote:

> Galt,
>
> Thanks for your reply. We are trying to display probe sets together. If
> we load each individual probe as a separate sequence, it is difficult to
> show which probes belong to the same set. So one way of doing that, we
> think, would be to use the whole probe set as the sequence and treat
> each probe as the exon. However, the central line makes it really look
> like the exon, which is confusing for the user because we only want them
> to be grouped but not "linked". Is there a way (parameter setting?) we
> can remove the central line? Or is there any suggestion of a different
> way of doing it? We need to apply it to only one track. Thanks so much
> for your time and help.
>
> Jin
>
>
> -----Original Message-----
> From: Galt Barber [mailto:galt at soe.ucsc.edu]
> Sent: Thursday, January 31, 2008 6:34 PM
> To: Ma, Jin
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] Question on the exon structure
>
>
> Could you please explain more about what you're trying to do?
>
> Do you need it to apply to everything or to just one
> custom/customized track?
>
> -Galt
>
>
> On Thu, 31 Jan 2008, Ma, Jin wrote:
>
> > Hi,
> >
> > I need your help on a question. Is there a way to remove or
> > significantly lighten the central line connecting all the exons for a
> > sequence (one row in the BED file)?
> >
> > Jin
> >
> >
> >
> >
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