Figure 8.

DiffSplice discovers alternative splicing variants present in the data. (a) Number of ASMs discovered by DiffSplice at different expression level. Besides ∼2400 ASMs that exactly match annotated ASMs, DiffSplice discovered >2000 ASMs, where only subsets of annotated splicing variants were present, nearly 200 ASMs with novel splicing variants added to annotated alternative splicing events and >700 ASMs that were completely new to the annotation. (b) Novel alternative splicing in gene STRA13, identified by DiffSplice but missed by Cufflinks both with and without annotation. DiffSplice discovered a novel exon in the annotated intron region between the second and the third exon of STRA13. Splice junctions evidenced that the exon was alternatively excluded (path 1) or included (path 2) in transcripts of this gene, and the skipping ratio was tested to have significantly decreased from Day 3 to Day 35.