Hello,
I am trying to analyse data from a CRISPR screening performed with GeCKO library v2; my experiment consists in 1 control and 3 treated samples, each with 3 biological replicates. I have already "counted" the number of sgRNAs for each of the fastq files in control and treated conditions. As a next step I would like to compare each treated condition to the control condition, to find the genes (and corresponding sgRNAs) that are positively enriched.
I tried using MAGeCK software to perform both counting and testing steps (test is performed with Robust Rank Aggregation method), but I can find very few positively enriched genes, with quite high p-values. I guess this could be due to the setup of my experiment, where most of the infected cells die and a very high number of sgRNAs have zero counts in the treated samples (the selection is very strong); I suspect the type of normalisation MAGeCk is doing is not suitable for such data.
Does anyone have any suggestion on how adapt MAGeCK test on such data, or any other idea on how to perform the analysis?
