SymSim – simulating multiple faceted variability in single cell RNA sequencing

The abundance of new computational methods for processing and interpreting transcriptomes at a single cell level raises the need for in silico platforms for evaluation and validation. Here, UC Berkeley researchers present SymSim, a simulator that explicitly models the processes that give rise to data observed in single cell RNA-Seq experiments. The components of the SymSim pipeline pertain to the three primary sources of variation in single cell RNA-Seq data: noise intrinsic to the process of transcription, extrinsic variation indicative of different cell states (both discrete and continuous), and technical variation due to low sensitivity and measurement noise and bias. The researchers demonstrate how SymSim can be used for benchmarking methods for clustering, differential expression and trajectory inference, and for examining the effects of various parameters on their performance. They also show how SymSim can be used to evaluate the number of cells required to detect a rare population under various scenarios.

Overview of SymSim

The true transcript counts, which are the number of molecules for each transcript in each cell at the time of analysis, are generated through the classical promoter kinetic model with parameters: promoter on rate (kon), off rate (koff) and RNA synthesis rate (s). The values of the kinetic parameters are determined by the product of gene-specific coefficients (termed gene effects) and cell-specific coefficients. The latter set of coefficients is termed extrinsic variability factors (EVF), and it is indicative of the cell state. The expected value of each EVF is determined in accordance to the position of the cell in a user-defined tree structure. The tree dictates the structure of the resulting cell–cell similarity map (which can be either discrete or continuous) since the distance between any two cells in the tree is proportional to the expected distance between their EVF values. For homogenous populations (represented by a single location in the tree), the EVFs are drawn iid from a distribution whose mean is the expected EVF value and variance is provided by the user. From the true transcript counts we explicitly simulate the key experimental steps of library preparation and sequencing, and obtain observed counts, which are read counts for full-length mRNA sequencing protocols, and UMI counts, otherwise

Zhang X, Xu C, Yosef N. (2019) Simulating multiple faceted variability in single cell RNA sequencing. Nat Commun 10(1):2611. [article]

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