Many tools can do this, such as ribopicker, blastn, sortmerna or rRNA selector, but it seems to not be very efficient in extracting the mRNA. This study focuses only on bacteria and Archaea.
Gong Zhang
What kind of RNA dataset? If you mean sequencing reads, try to use FANSe2 algorithm to map these reads to all kinds of bacterial and archeal RNA reference sequences with high error allowance (12~20%).
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