[Bioc-devel] About Hg38 BSgenome

Raffaele Adolfo Calogero raffaele.calogero at unito.it
Thu Dec 4 01:21:15 CET 2014

Hi Julian,

many thanks for the kind explanation it was very useful.

I will use your suggestion also because I am working only with
toplevel chromosomes.



>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).


Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
Via Nizza 52, Torino 10126
Tel.   ++39 0116706457
Fax    ++39 0112366457
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele.calogero at gmail.com
www:   http://www.bioinformatica.unito.it

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