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 CLC Genomics Workbench.

The tool for creating a fold-change track can be found here:

        Toolbox | Legacy Tools | Create Fold Change Track (Image create_expression_comparison_track_16_n_p)

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 33.14, and click on the button labeled Next.

Image create_fold_change_track_input_selection
Figure 33.14: Choosing the case expression track for the Create Fold Change Track tool.

You are now presented with the wizard step shown in figure 33.15 where you can set the following input parameters:

Image create_fold_change_track_wizardstep
Figure 33.15: Setting the input parameters for the Create Fold Change Track tool.

When finished with setting the parameters, click Next.

The Create Fold Change Track tool will produce an annotation track, including the genes or transcripts that were not filtered out based on the filtering criteria. Each feature in this track is annotated with the following information:

As is the case with all annotation tracks in the CLC Genomics Workbench, it is possible to sort and filter the results based on any of the above values, and to create track lists for further analysis of the results.