Detect alternative splicing Discover new genes Chr 11 Tying it all together: Detect alternative splicing Chr 19 Spliceform 1 Spliceform 2 Tying it all together: In this module we have learned about alignment and quantification of RNA-seq reads. While these steps are important, we really want to learn something about biology. To close out this module, we will see how RNA-seq can help us discover new genes and detect alternative splicing. Both of these functions are important for learning about how our bodies work and for treating disease.

Chr 11 Discover new genes: a Predicted gene Researchers use RNA-seq to find hundreds of new RNA transcripts . Many of these are far from known genes and appear to be involved in many different biological processes and diseases like development and cancer. Discover new genes: Here we see many RNA-seq reads (including a few spliced alignments) mapping to the genome at a location not overlapped by any known gene. Based upon the locations of the reads and the splice alignments, we can predict that these reads come from a new gene with two exons. Now that we know this new gene exists, we can try to study what it does.

Many human diseases, like cancer and muscular dystrophy, cause changes in RNA splicing patterns. By looking for these changes with RNA-seq, scientists hope to detect illness earlier and learn how diseases affect people differently. Spliceform 2 Spliceform 1 Spliceform quantification Alt splicing: Biomarker in muscular dystrophy for severity and cancer Chr 19 Spliceform 1 Spliceform 2 Detect alternative splicing: In this case, we have a gene with two spliceforms. By looking at the junction aligned reads, we can see that both of these spliceforms are expressed in our RNA sample. From these data, it appears that there are more copies of spliceform 2 than spliceform 1.