Analyzing CRISPR and RNAi genome wide screens

Question

[spacemorrissey]

I have data from genome wide CRISPR and RNAi gene knockdown screens. These were pooled experiments where genes were either knocked out with CRISPR or knocked down with RNAi, and then the surviving cells were sequenced. Tags corresponding to lethal knockouts would therefore be depleted in the resulting sequencing run. Does anyone know of a tool that will allow me to calculate a meta pvalue to combine the results of multiple experiments of this type?

[spacemorrissey]

I found this paper "Systematic comparison of CRISPR-Cas9 and RNAi screens for essential genes" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4900911/

Has anyone used this? Has anyone found anything better?

Answer 1

[Meisam]

I'm late to the party but in case someone has the same question: one practical approach is using rank-based methods to meta-analyse your screens, which basically bypass the need to individually normalise the enrichment scores between the screens. There are different methods but one convenient way to do it is via GeneRaMeN.

[Disclaimer: I am an author of this tool]