Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution

In this work, we propose a novel statistical "genome- guided" method called "Transciptome Reconstruction us- ing Integer Programing" (TRIP) that incorporates fragment length distribution into novel transcript reconstruction from paired-end RNA-Seq reads. To reconstruct novel transcipts, we create a splice graph based an exact annotation of exon boundaries and RNA-Seq reads. The exact annotation of exons can be obtained from annotation databases (e.g., Ensembl) or can be inferred from aligned RNA-Seq reads. A splice graph is a directed acyclic graph (DAG), whose vertices represent exons and edges represent splicing events. We enumerate all maximal paths in the splice graph using adepth-first-search (DFS) algorithm. These paths correspond to putative transcripts and are the input for the TRIP algorithm.