I get how to identify the genes with statistically significant alternative splicing from the Cufflinks/Cuffdiff splicing.diff file. However, I now want to experimentally validate this alternative splicing. The gene listed in the splicing.diff file has 5 transcript isoforms made up of 4-6 exons some of which have slightly different boundaries in a particular isoform. (Information I gleaned from the .gtf annotation file produced by cuffmerge)
To design qRTPCR experiments to validate the alternative splicing it would be very helpful if I knew which splice sites to go after in my experiments. I can not seem to get this information from the analysis output. Am I missing something simple here.
Thank you for any assistance you can give.
To design qRTPCR experiments to validate the alternative splicing it would be very helpful if I knew which splice sites to go after in my experiments. I can not seem to get this information from the analysis output. Am I missing something simple here.
Thank you for any assistance you can give.
