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
