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RNA-Seq uses the number of sequencing reads per gene or transcript to quantify gene expression. Once reads are aligned to a reference genome, we need to assign each read to a known transcript or gene to give a read-count per transcript or gene. 

• Select Click the Aligned reads data node
• Select Quantification from the task Click Quantification in the task menu

We will use Partek E/M to quantify reads to an annotation model in this tutorial. For more information about the other quantification options, please see the Quantification user guide. 

• Select Click Quantify to an annotation model (Partek E/M) (Figure 1)
  
  

• Select RefSeq Choose the latest RefSeq Transcripts annotation from the Gene/feature annotation drop-down menu
• Select Click Finish (Figure 2)
  
  

The Quantify to annotation model task node outputs two data nodes, Gene counts and Transcript counts (Figure 3). 

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To view the results of quantification, we can select either data node output. 

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