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Katsevich-Lab / sceptre

An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.
https://katsevich-lab.github.io/sceptre/
GNU General Public License v3.0
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non-targeting gRNAs #151

Closed nhu-github closed 1 month ago

nhu-github commented 1 month ago

How to make the pipeline run if I have only one non-targeting gRNAs present?

See error message below: ---- Command error: Note: If you are on a Mac laptop or desktop, consider setting parallel = TRUE to improve speed. Otherwise, keep parallel = FALSE.

Error in check_calibration_check_inputs(sceptre_object, n_calibration_pairs, : Two or more non-targeting gRNAs must be present to run the calibration check when using the NT cells as the control group. gRNAs that are non-targeting should be assigned a gRNA group label of 'non-targeting' in the grna_target_data_frame. Calls: do.call -> -> check_calibration_check_inputs Execution halted

timothy-barry commented 1 month ago

Hey Nan,

Are you running a low-MOI analysis in which you are using the NT cells as your control group? In this case, you will not be able to run a calibration check if you have only a single NT gRNA. My recommendation would be to skip the calibration check and just go straight to the power check and discovery analysis. In general we would recommend using at least ~10 NT gRNAs, if possible.