We have learned about alignment and quantification of RNA-seq reads. While these steps are necessary, we really want to learn something about biology!
In Activity 4, we will see how RNA-seq helps us discover new genes and detect alternative splicing. Both functions are important for learning about how our bodies work and for treating disease.
1. What would be a reasonable hypothesis if you had a lot of RNA reads align with a part of the genome containing no known genes?
2. RNA-seq can identify different spliceforms. What were the example diseases that can change RNA splicing?
3. How does RNA-seq allow you to see how much of one type of spliceform is expressed compared to another type of spliceform? Hint: If you have your aligned reads for the spliceforms, what would you do next to compare the two spliceforms?