[Bioc-devel] Can we get a rheMac2 BSgenome?

[Hervé Pagès]

On 03/28/2012 03:05 PM, Hervé Pagès wrote:
> Hi Steve,
>
> On 03/27/2012 01:10 PM, Steve Lianoglou wrote:
>> For what it's worth, I whipped up a rheMac2 BSgenome object.
>>
>> The source package is here:
>>
>> http://cbio.mskcc.org/Public/Leslie/lianos/bioc2012/BSgenome.Mmulatta.UCSC.rheMac2.tar.gz
>>
>>
>> The data I used to create it along w/ the seed file is here. Maybe it
>> will be helpful as a starting point if you guys want to whip one
>> together officially:
>>
>> http://cbio.mskcc.org/Public/Leslie/lianos/bioc2012/rheMac2.BSgenome-data.tgz
>>
>
> Thanks! I'll check this and add it to the repo.

Done. BSgenome.Mmulatta.UCSC.rheMac2 should become available for
BioC 2.10 users in less than 1 hour. The TRF masks are non-standard
but I added them anyway (with a NOTE). I also added a view for Macaca
mulatta to the biocViews package but I don't know how long this one
will take to propagate.

Cheers,
H.

>
> Cheers,
> H.
>
>>
>> I'm not sure if I got all the mask stuff right, so ... use at your own
>> risk. I'll be pulling those things down by the end of the week or so.
>>
>> -steve
>>
>>
>> On Tue, Mar 27, 2012 at 12:11 PM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com> wrote:
>>> Howdy,
>>>
>>> How does bioc-core feel about hosting a BSgenome for the rhesus macaque?
>>>
>>> I'm taking a shot at forging my own now, but I guess it might be
>>> generally useful (but perhaps not, since it hasn't landed in bioc
>>> yet).
>>>
>>> Anyway, I'd be happy to send over a drop of the raw/source package w/
>>> required data to whomever if it'll be helpful to get the genome "live"
>>> for more people.
>>>
>>> -steve
>>>
>>>
>>> --
>>> Steve Lianoglou
>>> Graduate Student: Computational Systems Biology
>>> | Memorial Sloan-Kettering Cancer Center
>>> | Weill Medical College of Cornell University
>>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
>>
>>
>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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