The directed graphical model used by RSEM. The model consists of N sets of random variables, one per sequenced RNA-Seq fragment. For fragment n, its parent transcript, length, start position, and orientation are represented by the latent variables Gn, Fn, Sn and On respectively. For PE data, the observed variables (shaded circles), are the read lengths ( and ), quality scores ( and ), and sequences ( and ). For SE data, , , and are unobserved. The primary parameters of the model are given by the vector θ, which represents the prior probabilities of a fragment being derived from each transcript.
Li and Dewey BMC Bioinformatics 2011 12:323 doi:10.1186/1471-2105-12-323