I would like to create a simple QC check of RNA-Seq data that simply maps the data to rRNA and then counts the number of reads that map.
I've done this manually for human using sequences for 5S, 5.8S, 18S, and 28S rRNA (rDNA, actually). I gathered those sequences manually to create a small fasta file to use as a reference and it worked well.
I would like to have a more definitive source for this reference though, and I don't necessarily want to use a species-specific database, so I thought that using a fasta file downloaded from SILVA would be great, but I don't know if I'm using the wrong fasta file or what. I'm not very familiar with SILVA, but I noticed that when I tested it using the same sequencing data, I got unexpectedly many fewer hits than I did with my manually created 4-sequence reference than with the SILVA NR99 fasta file.
So I blasted my 4 rDNA sequences against the SILVA NR99 data and only the 18S was found. The others (5S, 5.8S, and 28S) don't appear to be there. Am I misunderstanding the nature of the SILVA project or could I be doing something wrong?
UPDATE: Please note, this question is about where to find rRNA and/or rDNA sequences to use as a reference, not about tools that can be employed in quantifying rRNA read content. While I appreciate hearing about tools that can generate nice reports about rRNA reads in an RNA-Seq run, the question is not answered unless it addresses the missing rRNA/rDNA sequences that are necessary for comprehensive quantification. Any tool can count rRNA/rDNA mappings, but the results will only be as good as the rRNA reference data supplied (unless it is a reference-less tool). And it's the lack of 5S, 18S, and 28S ribosomal subunits in SILVA that is my main concern. It's the difference between 1k reads and 500k reads mapping to rRNA/rDNA sequences.