How to visualize transcript alignments

Sorry readers,
Was very busy with my work so couldn't post any updates.
Lately I've been working with human cancer transcriptome assemblies. I mainly wanted to find out the changes in 3'end of the assembled transcripts as compared with the "reference" (normal transcripts). I aligned my short reads to the Cufflinks assembled transcripts using BWA.
Then the question is how do I visualize the alignments. There are plenty of visualizer to visualize reference genome alignment but couldn't find anything for transcripts (may be didn't search hard enough for it).
Then I though of using the sequences of assembled transcripts as reference only and imported them to IGV (Integrated Genome Viewer) and also imported my BWA alignments in BAM format. It works and I can see where poly-A tails are presens (representing the 3' end of the transcript).
The only glitch is that I can see only one assembled transcript at a time. Anyways.. small trick.. but solved my purpose.