[BioC] BSgenome.Ggallus.UCSC.galGal3 missing chromosomes?

[Hervé Pagès]

Hi Martin,

Good catch. I've no idea why chromosomes 21-28 are missing.
BSgenome.Ggallus.UCSC.galGal3 was packaged a long time ago (about
3-4 years) and, sadly, it seems that those chromosomes have been
missing from the beginning.

I've just repackaged version 1.3.18 of the package with all the
missing chromosomes. It's only available as a source package and
in the devel version of BioC for now:

 
http://bioconductor.org/packages/2.11/data/annotation/html/BSgenome.Ggallus.UCSC.galGal3.html

If you are on Mac or Windows, you can install with
biocLite(..., type="source").

Please let me know if you find any other issue down the road.

Thanks,
H.


On 05/10/2012 04:43 AM, Martin Johnsson wrote:
> Dear Mailing List,
>
> I'm a PhD student happily using Bioconductor (especially Biostrings) for
> some sequence analysis in the chicken. I would like to use the
> BSgenome.Ggallus.UCSC.galGal3 package, but chromosomes 21-28 don't seem
> to be included. I just upgraded to version 1.3.17 of the package and
> 2.15.0 of R.
>
> When googling around, I've found some email exchanges mentioning
> microchromosomes missing from the assembly, and that they (of course)
> won't be in the package either. However, the chromosomes in question are
> available in genome browsers, and as chr21.fa etc. from the UCSC
> chromFa.tar.gz file that the package manual refers to.
>
> Any pointers would be helpful -- is building a new version of Ggallus
> BSGenomes package myself the way to go?
>
>
> Sincerely,
>
> Martin Johnsson
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Hervé Pagès

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