[BioC] adding papaya genome to BSgenome

[Martin Morgan]

On 2/15/2013 4:19 PM, Hervé Pagès wrote:
> Hi Rishi,
>
> Papaya not being a model organism, it's hard for us to justify putting
> resources on supporting a BSgenome package for it. Have you tried to
> make your own BSgenome package? Please have a look at the BSgenomeForge
> vignette in the BSgenome *software* package for how to do this. Let us
> know if you run into problems and need help with this.

Also, a lighter-weight solution might use Rsamtools::FaFile to access the fasta 
sequences using, e.g., getSeq().

Martin

>
> Cheers,
> H.
>
>
> On 02/04/2013 09:34 AM, Rishi [guest] wrote:
>> I foud the MeDIP seq analysis in your package very interesting to me but my
>> genome (papaya) was not listed there. The genome is available on phytozome
>> http://www.phytozome.net/cgi-bin/gbrowse/papaya/
>>
>> ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Cpapaya/
>>
>> Is there anyway you can add the papaya genome to the BSgenome package
>>
>> Rishi Aryal
>> Department of Plant biology
>> University of Illinois at Urbana-Champaign
>>
>>   -- output of sessionInfo():
>>
>> aaa
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109