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Now that the data has been imported, we need to make a few changes to the data annotation before analysis. 

Modifying Sample Attributes

Notice that the Sample ID names in column 1 are gray (Figure 1). This indicates that Sample ID is a text factor. Text factors cannot be used as a variable in downstream analysis so we need to change Sample ID to a categorical factor. 

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The samples names in column 1 are now black, indicating that they have been changed to a categorical variable. Next, we will add attributes for grouping the data. 

Adding Sample Attributes

• From the RNA-seq workflow panel, select Add sample attribute to bring up the Add Sample Attributes dialog (Figure 4)
  
  

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The attribute will now appear as a new column in the RNA-seq spreadsheet with the heading Tissue and the groups muscle and not muscle. 

Choosing Sample ID Column

The next available step in the Import panel of the RNA-seq workflow is Choose Sample ID Column. Verifying the correct column is designated the Sample ID becomes particularly important when data from multiple experiments is being combined.  

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Performing QA/QC

The next step is to assess the quality of the data by checking the alignments per read. 

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