[Genome] problem with custom tracks

[Kate Rosenbloom]

Hello Gabor,

The custom tracks mechanism currently has no method of directly
determining which assembly the coordinates in a custom track file
are referencing.  (We are in the process of adding features to
handle this.)  The problem that you are seeing sounds like the
effect of loading a custom track into the incorrect assembly.
 From our internal representation of your tracks (the trash file, below),
it appears that the custom track files you are loading
contain mm7 coordinates, and so include chromosomes not
valid for mm8.

I was not able to reproduce your problem with Example 6
in our User's Guide.  This may also be a case of loading into
the wrong assembly.  If you could send me the output of
http:/genome.ucsc.edu/cgi-bin/cartDump, I could see if
this is the cause.

If you're still having problems, please contact me directly.

    Cheers,
	Kate
---
Kate Rosenbloom
UCSC Genome Bioinformatics

Gabor Bartha wrote:
> I am having problems with custom tracks and while testing noticed that this also affects the example given in your help for psl tracks.  
> 
> http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr7&hgt.customText=http://genome.ucsc.edu/goldenPath/help/ct_example6.txt
> 
> For the example the problem seems to occur on my Linux machine but not on my windows machine.  The error for the example is:
> 
> Error line 592 of ../trash/ct/ct_genome_5a2c_b01ff0.bed:chrY_random not a chromosome
> 
>  
> 
> The error I get is similar - it refers to a .bed file and not the .psl file used for the custom track and if refers to a chromosome that is not in the .psl file.  My example fails on both machines for mm8.  I am using Firefox if that makes any difference.
> 
>  
> 
> Gábor Bartha, Ph.D.
> 
> Director of Information Sciences
> 
> Synergenics, LLC
> 
> 863 Mitten Rd., Suite 101
> 
> Burlingame, CA 94010
> 
> 650-259-5000 x256
> 
>  
> 
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