How many cell lines needed for P-value calculation?

[ysun25]

My data set so far contains only 2 cell lines and 1 pDNA control. Jacks could generate the per gene results and stds but not P-values were generated. I'm guessing that's because I have to few cell lines in the data set. Is that correct? How many cell lines are needed for it to calculate P-values? Thanks!

[felicityallen]

Hi, the number of cell lines doesn't matter for this. To get a p-value, you need to set the --ctrl_genes input when you run JACKS. This should specify either a single gene (e.g. INTERGENIC) or a file containing a list of genes that are negative controls for your phenotype i.e. guides targeting genes or intergenic regions where you do expect Cas9 to cut DNA, but where you don't expect these genes or regions to have an effect on the phenotype of interest. If these are survival screens, the Non-Essential gene set defined by Traver Hart are usually a reasonable choice.

[ysun25]

Got it. Thanks!