Procedures for pooled sgRNA screening analysis.

1. QC: fastqc
2. Trim: cutadapt
3. Reads mapping: bowtie
4. Counts: count_sgRNAFsam.py
5. Quantile normalization: quan_norm.r
6. Basic quality check: whether sgRNAs targeting essential genes are depleted in transduced cells from input plasmid library? Whether sgRNAs targeting known hits are enriched?
7. Comparison methods: a. Z-score b. Gene differential expression c. RIGER d. STAR e. MaGeck

sgRNA_density.R: for ploting the density of sgRNA log2 fold change and displaying the sgRNA LCF of topgenes volcano_plot.R: for volcano plot of all genes, and label some top genes.