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Careful design in the primary steps of a next-generation sequencing study is critical for obtaining successful results in downstream analysis. In this study, a framework is proposed to evaluate and improve the sequence mapping in targeted regions of the reference genome. In this regard, simulated short reads were produced from the coding regions of the human genome and mapped to a Customized Target-Based Reference (CTBR) by the alignment tools that have been introduced recently. The short reads produced by different sequencing technolog

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We find that these steps are also useful in establishing a treatment ranking; Minocycline, a therapy with no significant findings in the OBTT analyses, yields the highest percentage recovery in our ranking. Furthermore, of the seven classifiers we have evaluated, Naïve Bayes achieves the best performance (67%) and yields significant improvement over our baseline model on the preprocessed dataset with borderline elimination. We also investigate the effect of testing on individual treatment groups to evaluate which groups are difficult to