I am analyzing RNA-seq data (not for the first time) but for a subset of samples I am getting a very low alignment rate (~30%). To find out what is going on I have looked at some of the unaligned reads and they seem to come from ribosomal RNA.
Now my question: Are ribosomal RNA sequences not contained in the standard reference genome sequence (e.g. hg19)? Is that why the reads did not align or should I be able to map rRNA reads to hg19?