Abstract: A system may include an alignment algorithm and a sample deep learning model configured to output screening maps. The system may also include executable computing instructions that cause one or more processors to receive a plurality of experiment datasets comprising respective unaligned sample perturbation readouts from samples transfected with CRISPR-Cas9 reagents and respective control readouts from control samples transfected with intron targeting control reagents. The one or more processors may also identify intron feature characteristics for the control readouts using the alignment algorithm and generate aligned sample perturbation readouts from the unaligned sample perturbation readouts using the alignment algorithm and the intron feature characteristics identified. The one or more processors may also generate a screening map for the plurality of experiment datasets centered around the control readouts by processing the aligned sample perturbation readouts through the sample deep learning model.