That sounds a promising solution. If I can give liftover a file of co- ordinates in MD£ and get Bta4 positions back (or vice versa) I would be very happy. A MD3 browser would make me ecstatic, but I cannot have everything in life.
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 6:22 PM, Angie Hinrichs wrote: > 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
