Tophat and unannotated transcripts

[honey]

I have two questions hopefully some one can help me:
I plan to use Tophat to align my RNA seq reads from mouse cell line and to check the expression of uannotated as well as annotated transcripts.

1. Has any one used Tophat for mouse transcriptome analysis? it works fine like that for human.
2. Will tophat and Cufflink give me both unnoatted as well as annotated transcripts/ genes.

Thanks

[kopi-o]

1. It works like it does for human experiments, in my experience.

2. Cufflinks can do that or not depending on how you run it. Please refer to the manual-