[Genome] Creating custom track similar to Affy all exon

[Kayla Smith]

Hello Michiel,

Here is a link to information on how to make a microarray custom track. 
  The example that will be useful to you is at the bottom of the page:

http://genomewiki.ucsc.edu/index.php/Microarray_track

You'll need to use a BED-15 format, and use the expNames variable for 
your sample names.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assitance.

Kayla Smith
UCSC Genome Bioinformatics Group


Michiel van Galen wrote:
> Hello,
> 
> I'm trying to create a custom track that kinda looks like the Affymetrix
> all exon track. I'm using the following BED format:
> 
> browser position chr22:1-20000
> track name=Test description="Test probes" visibility=3 itemRgb=On
> chr22   2000    5000    Smple1    0       +       2000    5000
> 245,0,0
> chr22   2000    5000    Smple2    0       +       2000    5000
> 200,0,0
> chr22   2000    5000    Smple3    0       +       2000    5000    50,0,0
> chr22   2000    5000    Smple4    0       +       2000    5000    10,0,0
> chr22   2000    5000    Smple5    0       +       2000    5000    0,0,43
> chr22   12000   15000   Smple1    0       +       12000   15000
> 150,0,0
> chr22   12000   15000   Smple2    0       +       12000   15000
> 0,122,0
> chr22   12000   15000   Smple3    0       +       12000   15000   0,12,0
> chr22   12000   15000   Smple4    0       +       12000   15000   54,0,0
> chr22   12000   15000   Smple5    0       +       12000   15000
> 0,102,0
> 
> This way the track is displayed as "Pack". The problem I have is that
> the sample names aren't only showed in front of the lines in the
> browser. Like it does when the visibilty option "Full" is selected. 
> 
> But when "Full" is selected the samples don't display on the same line
> anymore, it creates additional lines when zooming out. So what I'm
> trying to do is having only as many lines as the number of samples
> unregarded the zoom level. (as "Squish" does) And having the sample
> names only in front of those lines (like "Full" does).
> 
> I hope someone can help me out, kind regards,
> 
> -Michiel.
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