[Bioc-devel] About Hg38 BSgenome

[Julian Gehring]

Hi Raffaele,

Ignore my last post completely, it was overly optimistic:

The 'BSgenome.Hsapiens.NCBI.GRCh38' package contains the genomic
sequence that is identical between GRCh38 and hg38.  The naming of the
chromosomes is different.  For the toplevel chromosomes, the names can
be easily converted:

  library(BSgenome.Hsapiens.NCBI.GRCh38)
  library(TxDb.Hsapiens.UCSC.hg38.knownGene)

  bs = BSgenome.Hsapiens.NCBI.GRCh38
  seqlevelsStyle(bs) = "UCSC" ## convert to UCSC style

  seqlevels(BSgenome.Hsapiens.NCBI.GRCh38)

  seqlevels(bs)
  seqlevels(TxDb.Hsapiens.UCSC.hg38.knownGene) 

However, this does not work for the non-toplevel chrs, e.g.:
'HSCHR19KIR_RP5_B_HAP_CTG3_1' does not have a corresponding sequence in
the 'TxDb.Hsapiens.UCSC.hg38.knownGene' (and also won't be converted).

Best
Julian


Julian Gehring (12/02/14 15:44):

> Hi Raffaele,
> You can find it under the name 
>   BSgenome.Hsapiens.NCBI.GRCh38
>   http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html (http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html)
> The naming of the chromosomes has been harmonized between UCSC and GRCh with the new release, so there should be no need for two versions at the genome level.
> Best
> Julian
> On Tue, Dec 2, 2014 at 15:12, Raffaele Adolfo Calogero  wrote:
> Dear Bioc Team,
> I am the maintainer of chimera package.
> Recently some of the users asked for the possibility to use chimera with
> fusions detected on hg38 human genome.
> I checked for the availability of hg38 as BSgenome but I did not find it in
> Bioc repository, as instead there is TxDb.Hsapiens.UCSC.hg38.knownGene. I
> would like to know if it is planned the release of hg38 as BSgenome, maybe
> in the next Bioc release.
> In case it is not planned could please suggest me what to read to build it?
> Cheers
> Raffaele