DNA stable isotope probing (DNA-SIP) allows for the identification of microbes that assimilate isotopically labeled substrates into DNA. Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP). MW-HR-SIP has improved accuracy over other methods and is easily implemented on the statistical platform R. We also discuss key experimental parameters to consider when designing DNA-SIP experiments and how these parameters affect accuracy of analysis.
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