[Genome] Bed file

[Ann Zweig]

Hello Alon,

	Sorry to hear that you're having problems with custom tracks.  Let me 
point you towards a few resources, and after reading through them, if 
you're still having problems, please feel free to write back to the list.

	There is a comprehensive User's Guide for the Custom Track tool here: 
http://genome.ucsc.edu/goldenPath/help/customTrack.html  The first 
section explains how to create a custom track, while the second section 
explains how to load it.

	For a simple example, try pasting the following custom track (BED type) 
into the main custom track page here: 
http://genome.ucsc.edu/cgi-bin/hgCustom

browser position chr22:20100000-20100900
track name=coords description="Chromosome coordinates list" visibility=2
chr22   20100000 20100100
chr22   20100011 20100200
chr22   20100215 20100400
chr22   20100350 20100500
chr22   20100700 20100800
chr22   20100700 20100900

	Be sure to choose "Human" and "Mar 2006".  Then press 'submit'.  This 
will take you to the "Manage Custom Tracks" screen.  From there, press 
on the 'chr22' in the Pos column to view this custom track in the Genome 
Browser.  It should appear at or near the top of the annotation tracks.

	Hope this, and the User's Guide are helpful to you.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Alon Goren wrote:
> To whom it may concern,
> 
> Even  thou I have tried hard, I didn't manage to understand how do I  
> make a bed file (or anyone of the other options to upload as a track).
> 
> Is it that complicated?
> 
> Thanks,
> 
> Alon. 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome