On Thu, Jun 10, 2010 at 9:22 AM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> wrote:

>  Dear bioc-sig-sequencing,
>
> To clarify my original email (Browser display question), I am working with
> the Arabidopsis genome, not included at the UCSC browser.  So would like to
> prepare a bed or bedGraph file for display on a 'local' UCSC browser.
>
>
It is possible to target an alternative UCSC browser installation, but that
would depend on the custom track stuff working the same. Use the "url"
parameter to browserSession().


> To use the export/import capability of rtracklayer, the vignette example
> exports from a RangedData object to a bed file (among other formats).
>
> Initially, I would read in an Eland aligned file of reads to an AlignedRead
> object.  I note in a workshop (slides 17 & 18 of CoverageEDA.pdf,
> http://bioconductor.org/packages/courses/seattle-01-2009/day3/CoverageEDA.pdf),
> that R can display 'coverage vs Index' from an Rle object, similar to
> browser displays.
>
> So can I convert such an Rle object to a RangedData object in order to use
> rtracklayer to export it to a bed(Graph) file?
>
>
Yes. In fact, this happens automatically. Just try calling export(rle,
"coverage.bedGraph").


Thanks,
> pterry@huskers.unl.edu
> P. Terry
>
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>
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