[BioC] Bos taurus genome

[Hervé Pagès]

Hi Terhi,

bosTau6 is now in Bioc devel (source package only):

Will be available via biocLite() in 1 hour or so. You'll need to use the
latest R-devel (i.e. latest R-3.0, still under development), and install
the development version of BioC (2.12) following the usual procedure.

However, note that BSgenome.Btaurus.UCSC.bosTau6 should also work with
the current BioC release (i.e. R-2.15 + BioC 2.11), even though it's
normally considered bad practice to mix stuff from different BioC
versions. You can install it with:

   install.packages("BSgenome.Btaurus.UCSC.bosTau6",
 
repos="http://bioconductor.org/packages/2.12/data/annotation")

assuming that you already have all the dependencies installed. Should
really be a 1 time exception, and only if installing/using
R-devel/Bioc-devel is not an option for you.

Cheers,
H.


On 01/08/2013 12:40 AM, Iso-Touru Terhi (MTT) wrote:
> Hi,
>
> I'd like to use bioconductor with the cattle data but found out that genome versions available (bosTau4 and bosTau3) do not match to my version. Could it be possible to add a new version, namely bosTau6 (http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=320552169&clade=mammal&org=Cow&db=bosTau6).
>
> with kind regards,
> Terhi Iso-Touru
>
> ---
> Terhi Iso-Touru
> MTT Agrifood Research Finland
> FI-31600 JOKIOINEN, FINLAND
> www.mtt.fi/experts/terhi_iso-touru
>

-- 
Hervé Pagès

Program in Computational Biology
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