In order to make a liftover, we'd have to have the assembly for md4, and if we had that, we wouldn't need this liftover!
-Galt Kayla Smith wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
