[BioC] New bosTau4 genome

[hpages at fhcrc.org]

Hi Miika and BioC list,

I've added bosTau4 (Cow) to our list of supported genomes.

Some important changes since bosTau3:
- all chromosome sequences have changed: they are about
   10% longer in bosTau4,
- there is now a chrM sequence,
- UCSC also provides the upstream sequences for bosTau4 so
   I've included them in BSgenome.Btaurus.UCSC.bosTau4
- I've included the full set of masks (assembly gaps, inter-contig
   ambiguities, RepeatMasker and Tandem Repeats Finder).

I've also made a new version of BSgenome.Btaurus.UCSC.bosTau3
(version 1.3.12) that includes the full set of masks (version
1.3.11 only had the masks of assembly gaps and inter-contig
ambiguities).

Those 2 new packages (BSgenome.Btaurus.UCSC.bosTau4 and
BSgenome.Btaurus.UCSC.bosTau4 1.3.12) are only available
in the current release (BioC 2.3) and as source packages
for now (the binary versions for Windows and Mac will follow
soon).

As always, check what genomes are available for your platform with:

   > library(BSgenome)
   > available.genomes()

or use the 'type' argument to check for a specific type of
package.

Cheers,
H.


Quoting hpages at fhcrc.org:

> Hi Miika,
>
> You are the first person to ask for it. UCSC has it too now:
>
>   http://genome.ucsc.edu/FAQ/FAQreleases
>
> which is good because it's always easier to use what they provide.
> I'll make it and add it to our repository as soon as possible and
> will post on the Bioconductor mailing list when it's done.
>
> Cheers,
> H.
>
> Quoting "Tapio, Miika (ILRI)" <M.Tapio at cgiar.org>:
>
>> Dear Herve,
>>
>> What is the update plan for BSgenome to have Btau4 assembly for cattle?
>> Now that NBCI has updated their data-bases to match the new assembly, I
>> assume you get many inquiries about it.
>>
>>
>>
>> Kind regards,
>>
>> Miika
>>
>>
>>
>>