On Thu, May 14, 2009 at 7:29 PM, Kasper Daniel Hansen <
khansen@stat.berkeley.edu> wrote:

> As far as I know USCS uses zero-based indexing of their genomes, R uses
> 1-based. What kind of conversion is being used by rtracklayer - I suspect
> none at all? It might be worthwhile to add a discussion about this somewhere
> in the vignette?


It is even slightly more complicated than that.  They use zero-based starts
and 1-based ends, except for graphical display:

http://genome.ucsc.edu/FAQ/FAQtracks#tracks1

Sean


>
>
> More specifically, I have downloaded a couple of tables from UCSC using
> rtracklayer and I wanted to know if I need to add 1 to the column named
> exonStart (after a suitable splitting - it is a comma separated character
> list).
>
> Kasper
>
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