Can Mixscape Analyze High MOI Data?

[Huifang-Xu]

Hello Seurat Team,

Thank you for developing such an amazing tool! I have a question regarding the multiplicity of infection (MOI) in my experimental setup. Specifically, our MOI is high (MOI = 8), meaning each cell may contain around eight guides. Is Mixscape applicable to high MOI data, and if so, do you have any recommendations or best practices for analyzing high MOI data? If Mixscape isn’t ideal for this type of experiment, could you suggest any other software suited for high MOI data?

Thank you in advance for your help and time.

Best regards,
Huifang

[mhkowalski]

Hi,

Mixscape doesn't natively support high MOI data.. This could be problematic if you are trying to learn a transcriptional response associated with individual genetic perturbations, but every cell has multiple genetic perturbations that have a transcriptional response.

I could imagine trying to learn a perturbation response using cells that received only single perturbations (if you have enough of those in your data), and then scoring cells with multiple guides based on these single-guide responses, but I don't have a better recommendation than that. This seems like an active area of ongoing work in the Perturb-seq field, so happy if others would weigh on this... I'm going to convert this to a discussion so that others can weigh in.