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).