The "Batch Coordinate Conversion (liftOver)" utility on the UCSC browser site 
supports lifting over calJac1 coordinates to calJac3. However, I do not see a 
calJac1ToCalJac3.over.chain in the download directory here:

http://hgdownload.cse.ucsc.edu/goldenPath/calJac1/liftOver/

Could you possibly post the liftover file to the above directory or point me to 
where I can download it?

Thanks,

Alan


R. Alan Harris, Ph.D.
Assistant Professor
Bioinformatics Research Laboratory
Epigenomics Data Analysis and Coordination Center
Department of Molecular and Human Genetics
Baylor College of Medicine
Houston, TX 77030
713-798-7695
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