On Thu, Jun 10, 2010 at 9:22 AM, [email protected] < [email protected]> 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, > [email protected] > P. Terry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
