Quantifying to an annotation model

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.

• Click the Aligned reads data node

• 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.

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

Figure 1. Invoking Quantify to an annotation model (Partek E/M)

We will use the default options for quantification. To learn more about the different options, please see the Quantify to annotation model (Partek E/M) user guide.

• Choose Ensembl Transcripts release 105 annotation from the Annotation model drop-down menu (you may need to download it first, via Library File Management or click Add annotation model from the bottom of the drop-down)

• Click Finish (Figure 2)

Figure 2. Configuring Quantify to annotation model (Partek E/M)

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

Figure 3. The Quantify to annotation model task produces annotation model dependent outputs (e.g. Gene counts and Transcript counts node)

To view the results of quantification, double-click an output data node to view the task report.

The task report details the number of reads within exons, introns, and intergenic regions. For detailed information about the quantification results, see the Quantify to annotation model (Partek E/M) user guide.

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