Workflow from Scientific Research

Schematic of the ZINB model developed to map Shigella genome-wide colonization factors in the presence of infection bottlenecks. Workflow shows the TraDIS raw dataset used for the sequential fitting of ZINB model parameters. The ZINB model was first applied to TIS in pseudogenes only to fit technical parameters (pairwise normalization factors and the dependence of stochastic mutant loss on input abundance rgk,in and the fraction of zeros in the output sample f z , r ). These fitted parameters were then used in a second ZINB model applied to all ~85,000 TIS to extract gene-wise log 2 FC values and determine significance.

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