Hello Harry, Making a liftOver seems like a reasonable request. I am passing this on to our developers, and I hope to get back to you soon as to the status of this data.
Kayla Smith UCSC Genome Bioinformatics Group ----- "Harry Noyes" <[email protected]> wrote: > Dear UCSC > As you probably know, the bovine community has got it self in to the > > unusual position of having two concurrent assemblies; Bta4 from the > Bovine Genome Consortium, that is the assembly used by UCSC, and MD3 > > put together by Steve Salzberg's group at University of Maryland. > Whilst MD3 is probably a better assembly, Bta4 is certainly better > annotated and supported. > > We are currently resequencing three bovine genome and I am aware of > other groups sequencing at least 11 more and we are all using MD3.0 > for mapping our short reads to the bovine genome. It would be very > useful for us and presumably for the other groups if we could have a > > liftover resource to map between the assemblies. I assume that there > > is already an over.chain for Bta4. Would it be possible to create an > > over.chain for MD3? If you could provide the over.chains we could run > > liftover. We could then host the mapping on our own servers and I > have had informal agreement to install other services on the Bovine > Genome Database server and I have approached them about running a > liftover service. > > Best of all would be if you could host the mapping at UCSC. > > The MD3 assembly is available from > ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/ > > I could request letters of support from the other groups sequencing > bovine genomes if that would help in your decision making. > > Best wishes > > Harry > > Harry Noyes > Room 231 BioSciences Building > University of Liverpool > Crown Street > Liverpool > L69 7ZB > 0151 795 4512 > www.genomics.liv.ac.uk/tryps > [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
