Hi! This is a CRISPR KO screen analysis-related question. I was using the crisprseq pipeline as a reference. I saw that it uses crisprcleaneR for CNV correction and normalization. I am not using it in my analysis; I am using the Mageck MLE's parameter (--cnv-norm) directly. If anyone has any insight into when to use crisprcleaneR instead of just using the default Mageck MLE option, I'd like to discuss. Secondly, if anyone has used Mageck MLE's option to perform CNV correction, I'd like to confirm the format of the matrix file from DepMap, as it has released updated files. Thank you for the help! -Kalyanee

Hi Kalyanee, Just a quick clarification first: CRISPRcleanR is an optional module in nf-core/crisprseq, not the default, so the pipeline will only use it if explicitly requested. Regarding its use: it can be very valuable when you expect strong genomic biases, such as broad CNV events or working with cell lines that have complex copy-number landscapes. In experiments where the genome is relatively stable, the benefit may be smaller. In my own analyses, I don’t apply it, but it’s definitely a tool to consider when working with cancer models. As for MAGECK CNV normalization option, I don’t have direct experience with it, and I’m not sure it is currently supported within the nf-core pipeline. If you’re interested in trying it out or would like to help evaluate or even develop support for it, that would be very welcome! Happy to discuss further if useful!