DGE-EM package can be used to infer gene expression levels from 3′-tag Digital Gene Expression (DGE) data. DGE-EM uses a novel expectation-maximization algorithm that takes into account alternative splicing isoforms and tags that map at multiple locations in the genome, and corrects for incomplete digestion and sequencing errors. Experimental results on real DGE data generated from reference RNA samples show that our algorithm outperforms commonly used estimation methods based on unique tag counting as well as estimates obtained from RNA-Seq data for the same samples. Results of a comprehensive simulation study assessing the effect of various experimental parameters suggest that further improvements in estimation accuracy could be achieved by optimizing protocol parameters such as the anchoring enzymes and digestion probability.
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
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M. Nicolae and I.I. Mandoiu,
Accurate Estimation of Gene Expression Levels from DGE Sequencing Data,
Invited talk, 1st Annual RECOMB Satellite Workshop on Massively Parallel Sequencing, March 26-27, 2011,