A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples.
BACKGROUND
Detecting and quantifying isoforms from RNA-seq data is an important but challenging task. The problem is often ill-posed, particularly at low coverage. One promising direction is to exploit several samples simultaneously.


RESULTS
We propose a new method for solving the isoform deconvolution problem jointly across several samples. We formulate a convex optimization problem that allows to share information between samples and that we solve efficiently. We demonstrate the benefits of combining several samples on simulated and real data, and show that our approach outperforms pooling strategies and methods based on integer programming.


CONCLUSIONS
Our convex formulation to jointly detect and quantify isoforms from RNA-seq data of multiple related samples is a computationally efficient approach to leverage the hypotheses that some isoforms are likely to be present in several samples. The software and source code are available at http://cbio.ensmp.fr/flipflop.
MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Fontainebleau, 77300, France. Elsa.Bernard@mines-paristech.fr.|Institut Curie, Paris, 75005, France. Elsa.Bernard@mines-paristech.fr.|INSERM U900, Paris, 75005, France. Elsa.Bernard@mines-paristech.fr.
Elsa
E
Bernard
Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France. laurent.jacob@univ-lyon1.fr.
Laurent
L
Jacob
Inria, LEAR Team, Laboratoire Jean Kuntzmann, CNRS, Université Grenoble Alpes, 655, Avenue de l'Europe, Montbonnot, 38330, France. julien.mairal.spam@m4x.org.
Julien
J
Mairal
Sysra, 91330, Yerres, France. viara@sysra.com.
Eric
E
Viara
MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Fontainebleau, 77300, France. Jean-Philippe.Vert@mines-paristech.fr.|Institut Curie, Paris, 75005, France. Jean-Philippe.Vert@mines-paristech.fr.|INSERM U900, Paris, 75005, France. Jean-Philippe.Vert@mines-paristech.fr.
Jean-Philippe
JP
Vert
D000465:Algorithms; D017398:Alternative Splicing; D006801:Humans; D020407:Internet; D012313:RNA / Q000378:metabolism*; D059368:RNA Isoforms / Q000032:analysis* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014584:User-Computer Interface
D059368:RNA Isoforms; D012313:RNA