Hi,
I know that alternative splicing is thought to depend on sequences in cis to the gene that is spliced, and there are several methods that find variants associated with alternative splicing influenced by a variant in cis (CuffDiff etc., reviewed in Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data), and also exciting new methods to find variants that influence splicing (http://www.ncbi.nlm.nih.gov/pubmed/25140736 and http://www.sciencemag.org/content/347/6218/1254806.abstract). I was wondering if the same methods can be applied to determine alternative splicing of distant genes (e.g. genes far away from the splice site), since some variants are thought to influence alternative splicing far away (for example, Rbfox doi: 10.1038/nsmb.2699). Does anybody know how we would find variants that influence splicing of trans-factors?
Thank you!
Francesca
