how to aligned to mouse pre-rRNA

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"Clean reads were first aligned to human or mouse pre-rRNA using Bowtie software (v.1.2.3)47, and the remaining unmapped reads
were then aligned to the human (hg19) or mouse (mm9) reference genome." from a paper
so,what should i do "Clean reads were first aligned to human or mouse pre-rRNA using Bowtie software"
thank you


RIP-seq

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