...

The Genome Viewer in the Partek Genomics Suite software can help you visualize enables visualization of differential expression and alternative splicing results in RNA-seq data. 

...

The viewer is almost identical to that seen after importing the aligned reads; the difference is the inclusion of the Isoform Proportions track (highlighted in the Tracks list in Figure 1). Next, we are going to view a single gene, SLC25A3, to understand how the Genome Viewer can help you visualize differential expression and alternative splicing results in RNA-seq datawith differentially expressed isoforms. 

• Type SLC25A3 in the Plot Position bar at the top of the window and hit Enter. The browser will browse to the gene (Figure 2)
  
  

...

SLC25A3 was reported by Wang, et al., (Nature, 2008) to have “mutually exclusive exons (MXEs)”. The reads mapped to the 3 transcripts of this gene in each of the tissue samples are shown in the Genome Viewer in the isoform proportion track. The relative abundances of the individual transcripts of this gene are shown by the height of the color coded bars on each transcript in the isoform proportion track. Note transcript NM_213611 has low expression while transcripts NM_005888 and NM_002635 have higher expression. Also note that NM_005888 is expressed primarily in the heart and muscle, indicated by the primarily green and orange bars, while NM_002635 is expressed primarily in the brain and liver, indicated by the primarily yellow and red bars.  

For additional tips on using the Genome Viewer, refer to Visualizing Mapped Reads with Genome Viewer.  

...