don't forget SNPlocs, where it is 'ch'

:-D


On Thu, Oct 4, 2012 at 12:10 PM, sun <fireflysrb@gmail.com> wrote:

> 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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>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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