Systems and methods for transcriptome analysis
The invention generally provides systems and methods for analysis of RNA-Seq reads in which an annotated reference is represented as a directed acyclic graph (DAG) or similar data structure. Features such as exons and introns from the reference provide nodes in the DAG and those features are linked as pairs in their canonical genomic order by edges. The DAG can scale to any size and can in fact be populated in the first instance by import from an extrinsic annotated reference.
1. A method of identifying an isoform, the method comprising:
obtaining from an annotated transcriptome database, using a computer system comprising a processor coupled to a non-transitory memory, a plurality of exons and introns from a genome;
using the processor to transform each of the plurality of exons and introns from the annotated transcriptome database into a node;
using the processor to create, for each pair of the plurality of exons and introns, an edge connecting the two members of the pair by their proximal ends, thereby transforming the plurality of exons and introns from the annotated transcriptome database into a directed acyclic data structure representing substantially all possible splice variants of the plurality of exons and introns wherein each and every pair of nodes is directly connected by at least one edge with no intervening nodes between that pair of nodes along that edge, wherein the directed acyclic data structure contains at least one pair of nodes connected by an edge that is not supported by evidence from the annotated transcriptome database;
storing the nodes and the edges as the directed acyclic data structure in the memory;
obtaining a plurality of sequence reads generated by sequencing a transcriptome of an organism; and
using the processor to align the plurality of sequence reads from the transcriptome to a path comprising a subset of the exons and introns connected by a subset of the edges, thereby identifying an isoform corresponding to the path as an isoform from the transcriptome of the organism.
2. The method of claim 1 , wherein using the processor to align the plurality of sequence reads comprises
calculating match scores between the plurality of sequence reads and the nodes in the directed acyclic data structure, and
looking backwards to predecessor nodes in the directed acyclic data structure to transform the plurality of sequence reads into a back-trace with an optimal score, wherein the back-trace with the optimal score is the path.
3. The method of claim 2 , wherein the edge for each pair of the plurality of exons and introns is created by the processor prior to aligning the transcript.
4. The method of claim 3 , further comprising representing each of substantially all of the exons from the genome as nodes.
5. The method of claim 1 , wherein the plurality of exons and introns comprises all of the exons of a gene.
6. The method of claim 1 , wherein the plurality of sequence reads further includes a novel exon, where novel exon means one that is found in the transcriptome and not in the annotated transcriptome database, and the method further comprises using the processor to create a new node in the directed acyclic structure to represent the novel exon, thereby transforming the directed acyclic structure to reflect discovery of the novel exon.
7. The method of claim 1 , wherein the nodes and edges in the directed acyclic data structure represent some known isoforms and some novel isoforms.
8. The method of claim 1 , wherein a one of the plurality of exons and introns and a second one of the plurality of exons and introns represent alternative versions of an exon differing by one codon.
9. The method of claim 1 , wherein a one of the plurality of exons and introns exists within a second one of the plurality of features on the genome.
10. The method of claim 1 , wherein the plurality of exons and introns includes at least 100 exons.