[Genome] Rat update and Cow dataset

[Brooke Rhead]

Hi again Donovan,

We went ahead and created the per-chromosome sequence downloads for bosTau3:

http://hgdownload.cse.ucsc.edu/goldenPath/bosTau3/chromosomes/

Please let us know if you have any issues using them.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Brooke Rhead wrote:
> Hello Donovan,
> 
> The Nov. 2004 (rn4) rat genome browser corresponds to the most recent
> sequence that is available (version 3.4 from Baylor).  An updated
> version will be released in the future, and when it is, we will make a
> browser for it.  The Baylor HGSC Rat Genome Project web page is located 
> here, if you are interested:
> 
> http://www.hgsc.bcm.tmc.edu/projects/rat/
> 
> Regarding the bosTau3 genome sequence, the reason we did not generate 
> the data set by chromosome is that there are a large number of scaffolds 
> in addition to the chromosomes.  Is the problem that the file is too 
> large to download?  If so, we would consider making smaller split files.
> 
> If you are able to download the file successfully but need tools to 
> extract just the chromosomes of interest from the fasta file, you can 
> use the "faSomeRecords" tool in the kent source tree, which is available 
> for free for academic, non-profit and personal use.  See this link for 
> information on downloading the source tree:
> 
> http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
> 
> If this solution does not work for you, please let us know.
> 
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> 
> 
> Donovan Chan wrote:
>> Hello,
>> I just had two quick question. First, I was wondering when a lastest
> version of the Rat genome would be uploaded. The last version (rn4) was
> back in Nov 2004. Second, concerning the cow genome sequence: Would it
> be possible to obtain the data set by Chromosome, instead of the full
> data set? I know in the bosTau2, the information is available, but the
> most recent version would be best. All the data sets have been of great
> help to my reserach. Thank you for all your help
>> Cheers
>> Donovan Chan
>>
>> _______________________________________________
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> 
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