Expression Studies Of Alternative/Splice Variants Of A Gene

Question

[jvknp]

hi 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

[Neilfws]

On StackOverflow this question would be closed as too open and vague. Suggest you improve it to avoid the same fate.

[aravind ramesh]

Elobarate your question...

[jvknp]

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).

Answer 1

[Steve Lianoglou]

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:

• DEXSeq: R | Publication
• BitSeq: Python | R | Publication
• Cufflinks: Software | Publication