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. Author manuscript; available in PMC: 2019 Nov 19.
Published in final edited form as: Nat Protoc. 2019 Feb 1;14(3):756–780. doi: 10.1038/s41596-018-0113-7

Figure 2. Example Quality control assessment of CRISPR/Cas9 screen data.

Figure 2.

All four samples analysed here are from a genome-wide CRISPR screen dataset generated from patient-derived Glioblastoma GBM stem-like cells (GSCs)20. These samples represent two conditions: Day0, initial time point of screen and Day23, after 23 days of culture. Replicate 1 and Replicate 2 are biological replicates. These results are generated by performing MAGeCK count. (a) Read counts and mapping percentages. The mapped read percentage should be greater than 65%. (b) pairwise sample correlations of read count, (c) Gini index, which measures read depth evenness within samples. (d) Number of missed sgRNAs.