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. Author manuscript; available in PMC: 2014 Oct 1.
Published in final edited form as: Nat Biotechnol. 2014 Mar 16;32(4):341–346. doi: 10.1038/nbt.2850

Figure 1. Element discovery overview.

Figure 1

(a) Exon discovery. For each gene segment we identify CAGE peaks; segment the gene region using the CAGE peaks, splice boundaries and poly(A) sites; label the segments based upon their boundaries; filter intron segments with low RNA-seq coverage; and build labeled exons from adjacent segments. (b) Transcript discovery. For each gene, we construct a graph where each node is an exon discovered in (b), and each edge is a junction. Then, each candidate transcript is identified with a single path through this directed graph that begins with TSS node, and ends with a TES node.