I have High-throughput sequencing data (cDNA from ribosomal profiling) and when I ran Fastqc on it and looked at the over-represented sequences, many of them were ribosomal genes. This is bad because the experimenters did use a protocol to remove the ribosomal RNA.
Now, I mapped the reads using Tophat, and now want to remove the instances that are mapped to the ribosomal genes. For this, I need a list of all ribosomal genes in rat, and then I can use samtools to remove the said reads. So, is there someplace I can find such a list?