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The Count normalization menu will open (Figure 2).

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Normalization can be performed by sample or by feature. By sample is selected by default; this is appropriate for the tutorial data set. 

Available normalization methods are listed in the left-hand panel. For more information about these options, please see the Normalization Normalize counts user guide.

For this tutorial, we will use the recommended default normalization settings.

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CPM (counts per million) normalizes read counts for each gene by the total count of the sample. This accounts for differences in total read counts between samples. 

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