TY - JOUR T1 - RNA-seq transcript quantification from reduced-representation data in recount2 JF - bioRxiv DO - 10.1101/247346 SP - 247346 AU - Jack M. Fu AU - Kai Kammers AU - Abhinav Nellore AU - Leonardo Collado-Torres AU - Jeffrey T. Leek AU - Margaret A. Taub Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/05/25/247346.abstract N2 - More than 70,000 short-read RNA-sequencing samples are publicly available through the recount2 project, a curated database of summary coverage data. However, no current methods can be directly applied to the reduced-representation information stored in this database to estimate transcript-level abundances. Here we present a linear model taking as input summary coverage of junctions and subdivided exons to output estimated abundances and associated uncertainty. We evaluate the performance of our model on simulated and real data, and provide a procedure to construct confidence intervals for estimates. ER -