search

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
248 stars 34 forks source link

Should I run this before or after imputation? #119

Closed ayeTown closed 1 year ago

ayeTown commented 1 year ago

Hi there, Should SoupX be run before or after imputation? I am using the ALRA methodology for imputation: https://github.com/KlugerLab/ALRA Thanks for your input. AT

constantAmateur commented 1 year ago

Run SoupX first, unless you have some particular reason to want to impute on contaminated data. If ALRA requires counts as inputs make sure to set roundToInt=TRUE when running adjustCounts