There is a middle ground: download the assembly, mask it for alignment, and create the liftOver chains, but don't do the rest of the work required to make a full genome browser for the assembly. I think the work of testing a new genome browser database for release is much greater than the effort required to make liftOver chains, or even to produce a browser on our test server.
Angie ----- "Galt Barber" <[email protected]> wrote: > From: "Galt Barber" <[email protected]> > To: "Kayla Smith" <[email protected]> > Cc: "Harry Noyes" <[email protected]>, [email protected] > Sent: Wednesday, November 18, 2009 10:06:29 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] over.chain for Bos Taurus MD3 assembly > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
