hi Jerry (and Harry), Thanks for your emails. We appreciate the fact that you use the UCSC Genome Browser, and in turn we try to provide the best possible support for our user community.
The existence of 2 competing bovine assemblies from different groups has posed a quandary for UCSC. We are funded and staffed to provide a browser on the NCBI reference assembly for this genome, which is currently the Btau_4.0 assembly from Baylor. Given the amount of work in our project queue and our lean staffing levels, generating and QAing a full browser on an alternative assembly would spread us thin and would require dropping other critical project tasks. It also requires a certain amount of customization on our part, since the Genome Browser isn't generally set up to provide alternative assembly versions of the same genome sequence release. I believe it's inevitable that we'll encounter this situation more and more as genome sequencing and assembly becomes cheaper and easier, and will therefore have to take it into account in future project planning and staffing. However, to provide the bovine community with a more immediate solution, Angie's proposal of simply downloading and masking the MD3.0 assembly, then producing liftOver chains with the Btau_4.0 assembly is our best option. Cheers, -Donna ---------------- Donna Karolchik UCSC Genome Browser Project Manager http://genome.ucsc.edu Taylor, Jerry F. wrote: > Angie: > > On behalf of the Animal Genomics group at the University of Missouri, I would > like to add my support to that of the remainder of the community for UCSC to > implement a full UMD3.0 bovine browser. This assembly is of higher quality > than the Btau4.0 assembly and has become the de facto standard for the > community. > > Regards, > > Jerry > > *********************************************************** > Jeremy Taylor > Professor and Wurdack Chair in Animal Genomics > S135 ASRC > University of Missouri > 920 East Campus Drive > Columbia, MO 65211-5300 > Voice: (573) 884-4946 > Fax: (573) 882-6827 > E-mail: [email protected]<mailto:[email protected]> > http://animalgenomics.missouri.edu<http://animalgenomics.missouri.edu/> > > "There is a general place in your brain, I think, reserved for 'the > melancholy of relationships past.' It grows and prospers as life progresses, > forcing you, finally, against your grain, to listen to country music." > > Kary Mullis - Nobel Prize lecture December 8, 1993. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
