[Bioc-devel] About Hg38 BSgenome

[Marc Carlson]

Hi Raffaele,

You are in luck today because while we normally do *not* have mechanisms 
to harmonize the non-standard chromosome names, for this specific case 
Herve wrote some code to handle it.  So you want to look at this:

library(GenomeInfoDb)
?fetchExtendedChromInfoFromUCSC


  Marc



On 12/02/2014 07:15 AM, Julian Gehring wrote:
> 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
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