[Bioc-devel] About Hg38 BSgenome

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