I've been tasked with trying to estimate how much of a sequence will align to known ribosomal RNA sequences. My current strategy is to create a ribosomal RNA intervals BED file and use that for Picard's CollectRnaSeqMetrics tool. I've actually Ribosomal Intervals For Collectrnaseqmetrics, but in this case I'm looking for C. elegans ribosomal RNA data.
If I can find any kind of data about what locations in the reference are rRNA, then I can make the BED file based on that. I've looked on the UCSC table browser, but I haven't found anything there. I also looked through the Illumina iGenomes FTP. I see in WormBook that the regions are known, but I don't see any specifics.
Does anyone know of any resources where I can find this information?