[BioC] BSgenome.Ggallus.UCSC.galGal3 missing chromosomes?
marjon at ifm.liu.se
Thu May 10 13:43:39 CEST 2012
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?
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