Interesting paper examines transcriptome reassembly and determines it is sensitive to RNA fragmentation technique. Concludes that Zn mediated fragmentation provides a better transcript ID compared to cleavage by RNase III: http://www.sciencedirect.com/science/article/pii/S1046202313000789

I wonder if this has been tested with Mg. Other methods to fragment nucleic acid: http://blog.genohub.com/fragmentation-of-dna-rna-for-next-gen-sequencing-library-prep/

-- Genohub