[Genome] Creating custom track similar to Affy all exon

Michiel van Galen m.van_galen at lumc.nl
Thu Nov 29 01:26:39 PST 2007


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.


More information about the Genome mailing list