[Genome] LiftOver question

[Pauline Fujita]

Hello Bob,

The liftOver utility only has a direct lift from the Mouse Jul. 2007 
release to the Feb. 2006 release and the liftOver menu only allows you 
to select pairs of assemblies for which there is a direct lift. You can, 
however, lift from Mouse July 2007 to other assemblies using repeated 
lifts (i.e. you could lift from Mouse July 2007 to August 2005 by first 
lifting from Jul. 2007 to Feb. 2006, and then lifting from Feb. 2006 to 
Aug. 2005). To lift from Human May 2004 to Mouse Jul. 2007 (build 37) 
you could lift:

  i) from Human May 2004 to Mouse Feb. 2006
  ii) then from Mouse Feb. 2006 to Mouse Jul. 2007

Hopefully this information was helpful and answers your question. If you 
have further questions or require clarification feel free to contact the 
mailing list at genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Bob Sinclair wrote:
> Hi,
>
> The liftover utility at http://genome.ucsc.edu/cgi-bin/hgLiftOver will 
> allow selection of the current (July 2007) mouse genome as "Original 
> Assembly" but only allows Feb 2006 as the new assembly when mouse is 
> selected as new genome. Is this an error on the page ir is there a 
> reason more recent mouse sequences cannot be selected as the new 
> assembly. (I'm trying to convert a group of ~800 coordinate pairs from 
> the May 04 human build to mouse build 37).
>
> Thanks, Bob.
>
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