Ribosomal RNA in RNA-seq data

Question

[lkmklsmn]

Hi biostars,
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?

Thanks!

[Chirag Nepal]

Reads mapping to rRNA are generally multi mappers and they might have been excluded due to the parameter you selected for mapping. In other words, did you allow multi mapping reads or not ? You could also directly map the reads only to rRNA and see what fraction of reads map to rRNA and how much reads are left ?

[lkmklsmn]

Thanks. Yes the percentage of multi-mapping reads is very high in those affected samples. Given that only a subset of the samples are affected by this (Alignment rate<50%) my conclusion is that there must have been some error in the rRNA depletion step.