I have some raw read count data from a crispr screen. The library used was addgene's

Mouse Improved Genome-wide Knockout CRISPR Library v2

I'm following an analysis pipeline that requires counts from non target gRNA in my raw read count file.

But the gRNA library does not contain non target gRNA.

I'm wondering what genes are commonly used as phenotypic controls in CRISPR screens?

In other words, what Genes, when mutated, does not affect the cell's fitness, thus can be used as a reference when comparing gRNA counts?

  • $\begingroup$ I would make this in a data-driven fashion. Check those genes that are canonically not expressed based on RNA-seq data in the cell type that was used here. The respective guides should have no impact and should serve as a proxy for the technical variability of the assay. $\endgroup$
    – user3051
    Nov 18, 2020 at 21:36


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