I am writing to seek your expertise in using CRISPRseeker tool to evaluate the accuracy and efficiency of CRISPR experiment.
Particularly, I am looking at "Scenario 5. Target and off-target analysis for gRNAs input by user" in the manual: http://bioconductor.org/packages/release/bioc/manuals/CRISPRseek/man/CRISPRseek.pdf
To briefly describe the experimental design, I have three biological replicates of target gene KO (using CRISPR/Cas) and control (non-target) samples from human cancer cell line. Running alignment and quantification using STAR results in very low counts for target gene in control samples, and higher counts in KO samples. I would really appreciate if you could provide some advice on leveraging CRISPRseeker tool to address this situation. Also, on how to interpret metric value for gRNAefficacy - does low value indicate low on-target rate?
I really appreciate all the help. Thanks