From Tracks to Experiments

When carrying out RNA-seq analysis using the RNA-Seq Analysis tool, the starting point is a set of reads from a sequencing study. As part of the RNA-Seq Analysis tool, these reads are mapped onto a reference genome. The RNA-Seq tool produces expression tracks, which are compatible with the reference genome, and can be visualized together with the genome in the Track List View (see Tracks). You can find more information about the RNA-Seq Analysis tool in RNA-Seq Analysis).

Once expression tracks have been obtained from the RNA-Seq Analysis tool, they can be used as sequencing-based sets of expression values in setting up an experiment. This can be done using the Set up Experiment tool, also found in the Transcriptomics toolbox. This is described in more detail in Experiments.

An experiment set up in this manner from expression tracks is intimately coupled to the tracks it originated from. To see this coupling in action, perform the following steps:

  1. Use the Set up Experiment tool on two or more expression tracks to set up an experiment, as described in Experiments.
  2. Save and open the resulting experiment, by double-clicking its name in the Navigation Area.
  3. Use the Create Track List tool to create a track list from the expression tracks you used to set up the experiment, as described in Tracks.

  4. Save and open the resulting track list by double-clicking its name in the Navigation Area.
  5. Drag the experiment tab downwards, until you see the blue shadow indicating the resulting placement (figure 28.64), and drop it in place. You should now have a divided view, with the experiment in the bottom half (figure 28.65).
  6. Clicking on any line in the experiment will now automatically jump to the corresponding genomic location in the upper view. Use the Zoom to Selection (Image zoom_selection) button to zoom in to the desired genomic region.

Image drag_tab_to_drop_genomics
Figure 28.63: Dragging a tab to the lower half of the view area.

Image two_panel_experiment_genomics
Figure 28.64: After dropping a tab to the lower half othe view area.

Image create_track_from_experiment_divided_view_1_genomics
Figure 28.65: Viewing the track produced by the Create Track from Experiment Tool

Image create_track_from_experiment_divided_view_2_genomics
Figure 28.66: The annotations on the track produced by the Create Track from Experiment Tool