Methods

Overview

The [ crispr_screen ] pipeline is really two analyses in one.

There is first the sgRNA enrichment analysis, and second the sgRNA aggregation analysis.

The reasoning for this is that we want to be able to determine which sgRNAs are statistically enriched/depleted in the treatments given the controls from their abundances. However, because there are generally such a high number of sgRNAs, there will be likely be many sgRNA hits that cross spuriously either statistically or biologically. If we were to just say that any gene with a statistically significant sgRNA was significantly enriched or depleted we will likely not end up with a set of genes which are robust in our assay.

sgRNA Enrichment

An overview of the sgRNA enrichment analysis is as follows:

• Normalize the read counts
• Fit the dispersion model
• Perform sgRNA-level enrichment
• Adjust p-values for multiple hypothesis correction

sgRNA Aggregation

An overview of the sgRNA aggregation procedure is as follows:

• Perform sgRNA aggregation (either αRRA or INC)
  • αRRA
  • INC
• Adjust p-values for multiple hypothesis correction