Hi All,

I am going to use "coding <- predictCoding(vcf, txdb, seqSource=Athaliana)"
to detect coding SNPs. The problem is that the chromosome names are not
consistent among VCF, txdb and BSgenome. In vcf, the chromosome name is
"Chr*", in txdb, the chr name is "Chr", but in BSgenome, the chr name is
"chr*" .

I know I can use renameSeqlevels() to adjust the seqlevels (chromosome
names) of the VCF object to match that of the txdb annotation. But how can
I adjust the chr name of BSgenome or TranscriptDB?

Thanks,

Rebecca

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