Expression tracks

Both tracks can be shown in a Table (Image table) and a Graphical (Image annotation_track_16_n_p) view. By creating a Track list, the graphical view can be shown together with the read mapping track and tracks from other samples:

        File | New | Track List (Image trackset_16_n_p)

Select the mapping and expression tracks of the samples you wish to visualize together and select the annotation tracks used as reference for the RNA-Seq and click Finish.

Once the track list is shown, double-click the label of the expression track to show it in a table view. Clicking a row in the table makes the track list view jump to that location, allowing for quick inspection of interesting parts of the RNA-Seq read mapping (see an example in figure 28.10).

Image mrna_seq_result_contig-web
Figure 28.10: RNA-Seq results shown in a split view with an expression track at the bottom and a track list with read mappings of two samples at the top.

Reads spanning two exons are shown with a dashed line between each end as shown in figure 28.10, and the thin solid line represents the connection between two reads in a pair.

When doing comparative analysis and opening an experiment (see Experimental design) and a track list, clicking a row in the experiment will cause the track list to jump to the corresponding position, allowing for quick inspection of the reads underlying the counts in the experiment. Please note that at least one of the expression tracks used in the experiment have to be included in the track list in order for the link between the two to work.

Expression tracks can also be used to annotate variants using the Annotate with Overlap Information tool. Select the variant track as input and annotate with the expression track. For variants inside genes or transcripts, information will be added about expression (counts, expression value etc) from the gene or transcript in the expression track. Read more about the annotation tool in Annotate with overlap information.

Gene-level expression
The gene-level expression track holds information about counts and expression values for each gene. It can be opened in a Table view (Image table) allowing sorting and filtering on all the information in the track (see figure 28.11 for an example subset of an expression track).

Image mrna_seq_result
Figure 28.11: A subset of a result of an RNA-Seq analysis on the gene level. Not all columns are shown in this figure

Each row in the table corresponds to a gene (or reference sequence, if the One reference sequence per transcript option was used). The corresponding counts and other information is shown for each gene:

Transcript-level expression
If the "Genome annotated with genes and transcripts" option is selected in figure 28.4, a transcript-level expression track is also generated.

The track can be opened in a Table view (Image table) allowing sorting and filtering on all the information in the track. Each row in the table corresponds to an mRNA annotation in the mRNA track used as reference.