[Bioc-devel] Can we get a rheMac2 BSgenome?
On 03/28/2012 03:05 PM, Herv? Pag?s 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
Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319