Hello, Harry,
We have released the liftOver tool to the public site. It
can
be accessed via the Utilites link off the main page or:
http://genome.ucsc.edu/util.html
and will lift coordinates from the UMD3 assembly to the
bosTau4
assembly.
best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On Wed, 18 Nov 2009 18:29:12 +0000
Harry Noyes <[email protected]> wrote:
> 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
>>
>>> 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 into 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 genomes 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
_______________________________________________
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