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

[Martin Johnsson]

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