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.
Cheers
Raf
>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
--
----------------------------------------
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.calog...@unito.it
raffaele.calog...@gmail.com
www: http://www.bioinformatica.unito.it
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