In my genome-wide CRISPR screen each gene in a certain cell-line was targeted by 4 sgRNA guides, and the resulting cells were injected to a WT, a WT+vehicle, and a WT+vehicle+drug set of animals. The guides were generated in 4 pools and each pool was then sequenced from the animal in a separate library, meaning that the sgRNA counts in a given sample differ among the 4 pools because of the different library depths. Another complication is that the 4 pools are not 100% identical WRT to the genes they target and not every gene is covered by all 4 pools, hence I have missing values (NAs, which if I try running MAGECK with it produces the Parsing error message and these lines are skipped).
Hi,
This is a usage question.
In my genome-wide CRISPR screen each gene in a certain cell-line was targeted by 4 sgRNA guides, and the resulting cells were injected to a WT, a WT+vehicle, and a WT+vehicle+drug set of animals. The guides were generated in 4 pools and each pool was then sequenced from the animal in a separate library, meaning that the sgRNA counts in a given sample differ among the 4 pools because of the different library depths. Another complication is that the 4 pools are not 100% identical WRT to the genes they target and not every gene is covered by all 4 pools, hence I have missing values (
NAs, which if I try runningMAGECKwith it produces theParsing errormessage and these lines are skipped).Any advice how to use
MAGECKfor these data?