MAGeCK-iNC (MAGeCK-including Negative Controls) is a bioinformatics pipeline for the analysis of pooled genetic screens created by Ruilin Tian, Kampmann Lab (2019).

This pipeline integrates a published method, MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout, Li et al., 2014) with aspects of our previous bioinformatics pipeline (Kampmann et al. 2013; Kampmann et al. 2014) to take full advantage of the non-targeting control sgRNAs in our libraries when computing P values.

Download the python script, including documentation, here.

Download an example input file here.

Download a script to convert counts files from the standard Kampmann Lab analysis pipeline to MaAGeCK-iNC input format here.

Download output files for the example input file here.

Run MAGeCK-iNC from the command line as shown:

MAGeCK-iNC screenshot
MAGeCK-iNC output

MAGeCK-iNC example output