Expression Analysis in Geneious Prime

This expression analysis series shows how to map RNA-Seq reads in Geneious Prime, calculate RPKM, FPKM, and TPM expression levels, and find differentially expressed genes between two sample conditions using confidence filtering and volcano plots. A third video covers running DESeq2 with biological replicates, including PCA plots and log2 fold change analysis.

Course Content

1. Calculating Expression Levels
Alternative: Expression Analysis with DESeq2

2. Measure Differential Expression

1. Calculating Expression Levels

Map each RNA-Seq read set separately to a reference, then run Calculate Expression Levels per sample assembly, never combining samples in one run. Review RPKM, FPKM, and TPM values on the color-coded expression track, or export the data as a CSV table.

LENGTH 5 minutes

2. Measure Differential Expression

Compare two expression tracks with Compare Expression Levels, using transcripts and median-ratio normalization. Filter the resulting track by confidence, such as greater than 2 for P < 0.01, and review results as a table or volcano plot..

LENGTH 6 minutes

Alternative: Expression Analysis with DESeq2

Map RNA-Seq replicates per sample condition, calculate expression levels for each, then compare them using the DESeq2 method, which installs R automatically on first use. Review the Log2 Ratio fold change, adjusted P-value, PCA plot, and volcano plot.

LENGTH 5 minutes