I am trying to find genes that express different isoforms in cancer vs normal RNA-seq data. The first thing that came to my mind was to do a differential expression analysis at exon level (I used edgeR for this)... then if I find a gene that express less number of exon compared to the annotation data for that gene, it means the gene is expressing a different isoform in cancer.
But this is clearly not the right way to do this, and I could not find any other way for this kind of analysis. I was wondering if someone has done this kind of analysis before can share his/her experience with me.
I really appreciate your help, Thanks, Sahel