single gene alternative splicing analysis

[frymor]

Hi everybody,

we are interested in analysing the possibilities of alternative splicing and different transcript length of a single gene.

For that I would like to download some RNA-seq data from human and mouse.

Do I need to download a complete data set (transcriptome) or is there a way to concentrate only on the location of the wanted gene?

Can someone recommend a software to do that kind of analysis. Can I use cufflink/cuffdiff to analyse it?

Thanks a lot in advance
Assa