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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)
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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 or mouse over the () next next to each option.
- Select RefSeq Choose the latest RefSeq Transcripts 95 annotation from the Gene/feature annotation drop-down menu Select (you may need to download it first, via Library File Management)
- Click Finish (Figure 2)
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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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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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