Covariate matrix?

[david...@gmail.com]

Dear Perturb-seq team,

How exactly is the covariate (design) matrix constructed for sgRNAs and/or other features?


Keep up the great work.
David

[Atray Dixit]

Hi David,

For the cell state covariate, see pg. e7 in our STAR methods section. Sections titled ("Definition of cell states", and "Relation of perturbed cells to unperturbed states") and the associated github example (https://github.com/asncd/MIMOSCA/tree/master/Cell_States) 

 

For the sgRNA covariates, see pg. e6 ("Alignment of cell barcode / GBC libraries") and the associated github example (https://github.com/asncd/MIMOSCA/tree/master/GBC_CBC_pairing) 

Let me know if you have any other questions,

Atray

[acellix...@gmail.com]

Hi Atray, 

   I'm still a little bit confused about how to get sgRNA covariates. I clicked the link that you mentioned above but I couldn't open it. Could you please explain the process? Thank you very much! 

Sincerely, 

Xinling Li