Simultaneous isoform discovery and quantification from RNA-seq.

ABSTRACT: RNA sequencing is a recent technology which has seen an explosion of methods addressing all levels of analysis, from read mapping to transcript assembly to differential expression modeling. In particular the discovery of isoforms at the transcript assembly stage is a complex problem and current approaches suffer from various limitations. For instance, many approaches use graphs to construct a minimal set of isoforms which covers the observed reads, then perform a separate algorithm to quantify the isoforms, which can result in a loss of power. Current methods also use ad-hoc solutions to deal with the vast number of possible isoforms which can be constructed from a given set of reads. Finally, while the need of taking into account features such as read pairing and sampling rate of reads ha

SUBMITTER: Hiller D 

PROVIDER: S-EPMC3718502 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature