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Table 1 Quality control (QC) measures from MAGeCK-VISPR

From: Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR

QC term Description Expected
GC content GC content distribution of the sequencing reads Similar distribution for all samples from same library
Base quality Base quality distribution of the sequencing reads Single-peak distribution with median base quality at least 25
Sequencing reads Total number of sequencing reads Varies depending on sequencing platform
Mapped reads Total number of reads mapped to the sgRNA library 300 * (number of sgRNAs)
% Mapped reads Percentage of mapped reads to the total number of sequencing reads At least 65 %
Zero sgRNAs Number of sgRNAs with zero read counts At most 1 % of total sgRNAs
Gini index Gini index of log-scaled read count distributions At most 0.1 for plasmid or initial state samples, and at most 0.2 for negative selection samples
Sample correlation Pearson correlation coefficient between samples At least 0.8 for replicates
Correlation clustering or PCA clustering Hierarchical clustering of samples or first three PCA components Samples with similar conditions should cluster together
Ribosomal gene selection Negative selection enrichment statistics of ribosomal genes Significant P values (<0.001) for ribosomal subunit (GO:0044391) in negative selection experiments