Create fold change track
The Create Fold Change Track tool can be used to compare RNA expression levels in two samples (e.g., matched tumor and normal samples).
After RNA-seq analysis, the resulting expression tracks can be compared using the Create Fold Change Track tool. For each gene or transcript, this tool will compute the ratio of the expression value in the case track to the expression value of the same gene in the control track. The tool enables filtering on the basis of fold-changes as well as expression values. This can give a quick first indication of possible differentially expressed genes or transcripts between two RNA-seq samples. For a more detailed and statistically robust analysis, we recommend running a Statistical Analysis tool in the Biomedical Genomics Workbench.
The tool for creating a fold-change track can be found here:
Toolbox | RNA-Seq Analysis (
) | Create Fold Change Track (
)
After starting the Create Fold Change Track tool, select the expression track corresponding to the case sample in the input dialog, as shown in figure 29.23, and click on the button labeled Next.
Figure 29.23: Choosing the case expression track for the Create Fold Change Track tool.