[Genome] Rat update and Cow dataset

[Brooke Rhead]

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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