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

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.Gg allus.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