Typical analysis workflow using TRACS to identify essential genes.

<p>(A) The TRACS workflow is separated into five steps. <i>Step 1</i>: Experiment parameters are entered in the graphical user interface (GUI). <i>Step 2</i>: Library reference file (.csv format) and raw read files (.fastq format) for all Cas9-positive replicates are selected in the GUI. <i>Step 3</i>: Raw read files (.fastq format) for all Cas9-negative replicates are selected in the GUI. <i>Step 4</i>: Raw reads are trimmed and aligned to generate read counts, then the TRACS algorithm runs to calculate Library ES, Initial ES, Final ES and the ER for each gene. <i>Step 5</i>: TRACS saves the results with all scores in an output file which can then be explored using the accompanying VisualizeTRACS data explorer. (B) Screenshot of the easy-to-use TRACS GUI asking user to enter experimental parameters (<i>Step 1</i>). Subsequent displays provide a similar interface for selecting input data files for <i>Steps 2–4</i>. (C-D) Screenshot of the accompanying VisualizeTRACS data explorer that researchers can use to visualize and inspect their TRACS output files and generate publication-ready figures. Researchers can control all aspects of filtering and data manipulation (Library ES, Initial ES, Final ES, ER, <i>p</i><sub><i>adj</i></sub>) to fine-tune selection of genes.</p> <p>(PDF)</p>