[BioC] BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)

[Hervé Pagès]

Hi Julie and other BSgenome users,

I've just made 2 new BSgenome data packages, one for ce10 (Oct. 2010,
WS220 assembly), and one for panTro3 (Oct. 2010, CGSC Build 2.1.3):

   BSgenome.Celegans.UCSC.ce10
   BSgenome.Ptroglodytes.UCSC.panTro3

The data in both packages were downloaded from:

   http://hgdownload.cse.ucsc.edu/downloads.html

Note that, strangely, ce10 is not listed in this table:

   http://genome.ucsc.edu/FAQ/FAQreleases.html#release1

The 2 new packages will become available for Bioc 2.11 users
(Bioc devel) via biocLite() in less than 1 hour. Only the "source"
packages are available for now. Windows and Mac users need to install
with biocLite( ... , type="source").

Please let me know if you have any question or find any issue with
those packages. Thanks!

Cheers,
H.

On 05/07/2012 08:00 AM, Zhu, Lihua (Julie) wrote:
> Herve,
>
> Hope all is well with you! Please let me know when the
> BSgenome.Celegans.UCSC.cd10 for WS220 is available for use.
>
> Many thanks!
>
> Best regards,
>
> Julie
>
> On 4/20/12 5:08 PM, "Julie Zhu"<julie.zhu at umassmed.edu>  wrote:
>
>> Herve,
>>
>> Great! Thanks so much for your kind help!
>>
>> Best regards,
>>
>> Julie
>>
>>
>> On 4/20/12 4:04 PM, "Hervé Pagès"<hpages at fhcrc.org>  wrote:
>>
>>> Hi Julie,
>>>
>>> On 04/20/2012 10:48 AM, Zhu, Lihua (Julie) wrote:
>>>> Herve,
>>>>
>>>> Is it possible to add BSgenome.Celegans.UCSC.ce10 for WS220 in the
>>>> Bioconductor release? Many thanks for your help!
>>>
>>> Sure. Given the number of sticky notes that are accumulating in front
>>> my eyes every day, it might take me a few days though. Thanks for your
>>> patience...
>>>
>>> Cheers,
>>> H.
>>>
>>>>
>>>> Best regards,
>>>>
>>>> Julie
>>>>
>>>>
>>>
>>
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>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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