[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.
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