Hi Galt Thanks for the answer but please could you expand a bit? Why isn't MD3 suitable for a lift over? Why would MD4 be suitable for a liftover if it did exist and why would the liftover be unnecessary?
I am sure that you are aware that the version numbers are not synchronised. Bta4 and MD3 are the current versions in each sequence of assemblies. 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] On Nov 18, 2009, at 6:06 PM, Galt Barber wrote: > 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
