Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data

摘要

Motivation: Estimation of isoform-level gene expression from RNA-seq data depends on simplifying assumptions, such as uniform read distribution, that are easily violated in real data. Such violations typically lead to biased estimates. Most existing methods provide bias correction step(s), which is based on biological considerations-such as GC content-and applied in single samples separately. The main problem is that not all biases are known.