how to identify which tissue has more alternative splicing?
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4.0 years ago
mail2steff ▴ 60

Dear all,

I am trying to identify AS events from different tissues (5 tissues). and I did that using rMATS. But now I need to know which tissue has the highest number of alternative splicing irrespective of events (mechanisms). I am kind of stuck in this. Can anyone guide me ?

rmats alternative splicing cuffdiff • 1.3k views
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4.0 years ago
petebio ▴ 40

I'm not sure exactly what you mean by "highest number of alternative splicing", but if you mean a higher number of isoforms expressed per gene then perhaps you could measure this using splicing entropy (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000011, https://www.ncbi.nlm.nih.gov/pubmed/25429061 ).

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Thank you for the reply. I will check on that link. For example, brain tissue has the highest number of alternative splicing compared to other tissues. In a similar way, I am interested to find the tissues in plants.

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