flexiMAP: A regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data

We present flexiMAP (flexible Modeling of Alternative PolyAdenylation), a new beta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data. Importantly, flexiMAP allows modeling of multiple known covariates that often confound the results of RNA-seq data analysis. We show, using simulated data, that flexiMAP is very specific and outperforms in sensitivity existing methods, especially at low fold changes. In addition, the tests on simulated data reveal some hitherto unrecognised caveats of existing methods.