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.
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? 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
