I detected thousands of genes in my RNA sequencing data. Why does the Singular Analysis Toolset display only a limited number of them?

By default, the Singular Analysis Toolset will display a limited number of genes, ranked by their principal component analysis score. This can be changed manually by selecting Find the top genes by this analysis in the autoAnalysis window and changing the desired number of genes to analyze. Alternatively, every transcript detected can be included in the analysis by selecting Defined in the expression file(s) from the autoAnalysis window. Note that increased processing time will be required for analyzing a large number of transcripts.