[Genome] error

[Kayla Smith]

Pavla,

The error you are getting: "chrX not a chromosome" suggests that your 
cart may have gotten confused, possibly when changing between different 
assemblies.  Try resetting your cart by using this url 
http://genome.ucsc.edu/cgi-bin/cartReset or by clicking on the Cart 
Reset option on the Gateway page as a temporary workaround for this 
problem.  We are currently in the process of improving our cart system. 
  If you could provide us with the exact scenario of what you were 
working on when you got this error, such as the steps you took to 
produce the error and whether you had created any custom tracks 
recently, it would be helpful.

Is it possible that you were converting from human (hg18) to zebrafish 
(danRer4) and the chr14 coordinates were the result that you got after 
converting from a region on hg18 to danRer4?  Therefore the chr14 
position is the result on danRer4 and the error would be after clicking 
on the link for that chr14 position.

That said, when I try to convert the coordinates chr14:65217037-65217157 
from human (hg18) to zebrafish (danRer4), after a cart reset, I get the 
message that "Sorry this position couldn't be found in new assembly". 
The region specified on chromosome 14 is not a very conserved region, so 
it is not surprising to find that it doesn't map to anywhere on danRer4.

You may find it useful to turn on the Zebrafish Net and Zebrafish Chain 
tracks in the Human browser and zoom out from your position.  This would 
allow you to see where nearby regions of human match up to zebrafish.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you have more questions.

Kayla Smith
UCSC Genome Bioinformatics Group


Pavla Navratilova wrote:
> Hi
> I have tried to convert one conserved region from human to zebrafish 
> sequence, but there was an error report
> 
> chr14:65217037-65217157 
> <http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=78871506&db=danRer4&position=chr14:65217037-65217157>
> 
> Error line 4667 of ../trash/ct/ct_genome_2524_bb7330.bed: chrX not a 
> chromosome
> 
> By BLATing on Zf I don't obtain any good hit :-(
> Can you somehow help me?
> Thanks
> Pavla Navratilova
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome