The IsoEM package can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. IsoEM uses a novel expectation-maximization algorithm that exploits read disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand, and read pairing information (if available). Empirical experiments on synthetic datasets show that the algorithm significantly outperforms existing methods of isoform and gene expression level estimation from RNA-Seq data, for details see our AMB paper.
IsoEM source code
The software is written in Java so it can be run on any platform with a java virtual machine. See the README.TXT file for installation instructions. The source code is distributed with the installation package.
Acknowledgment and Disclaimer
This material is based upon work supported in part by the National Science Foundation under Grants No. IIS-0546457, IIS-0916401, and IIS-0916948. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.