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

Hervé Pagès hpages at fhcrc.org
Mon May 14 18:18:09 CEST 2012

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:


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.


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
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Hervé Pagès

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