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 |