Dear Greg, Thanks a lot for your reply.
We cannot use http://genome.ucsc.edu/cgi-bin/hgLiftOver to select conversion from panTro3 to panTro2 (the other way works somehow). Are we missing something? Please let me know. All the best, Omer On May 31, 2011, at 2:51 PM, Greg Roe wrote: > Hi Omer, > > Ensembl has not produced a gene set for panTro3 (only panTro2: > http://uswest.ensembl.org/Pan_troglodytes/Info/Index/). You will need to > contact them with any questions about when/if one might be available. Were > you having troubles using the Ensembl track on panTro2? If so, please > describe the issue you are having in as much detail as possible. > > Regarding the liftOver. I just checked and liftOver between panTro3 <-> > panTro2 is working fine (http://genome.ucsc.edu/cgi-bin/hgLiftOver). Can you > please let us know what the exact problem you're having is? > > - > Greg Roe > UCSC Genome Bioinformatics Group > > On 5/30/11 5:06 AM, Omer Gokcumen wrote: >> Dear Sir/Madam, >> >> We are working on primate genomes and heavily using UCSC Genome browser. >> However, we are having difficulties lifting over between panTro2 and panTro3 >> genomic coordinates. In addition, we are not able to use the Ensembl track >> for annotating the genes on that genome. Is it possible for you to inform us >> regarding the dates that you are planning to implement these >> functions/tracks? Alternatively, it would be great if you can let us know if >> we are missing something regarding these issues. >> >> Thanks a lot in advance for your help. >> >> All the best, >> Omer >> >> >> >> >> ---------------------- >> Omer Gokcumen, Ph.D. >> Team Leader - Population Genetics and Evolution >> Molecular Genetic Research Unit >> Brigham&Women's Hospital | Harvard Medical School >> 221 Longwood Avenue, EBRC-404 >> Boston, MA 02115 >> T: 617.732.5316 | F: 617.264.5176 >> www.gokcumen.wordpress.com >> [email protected] >> [email protected] >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
