is there any sophisticated method (other than Real Time PCR) to study the expression of splice variants of a gene which differ by one or two codons
On StackOverflow this question would be closed as too open and vague. Suggest you improve it to avoid the same fate.
Elobarate your question...
I was studying the relative abundance of two splice variants (mRNA) under different stress conditions by qPCR. These two splice variants differ by one codon (revealed by RNA-seq data).
I'm not sure what you are really asking ("sophisticated method" is a bit vague), but there are several approaches to study changes in splicing using RNA-seq data, such as: