Using SoupX for dropseq data

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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Using SoupX for dropseq data #11

Closed yolsan closed 5 years ago

yolsan commented 5 years ago

Hi, I would like to use SoupX for my dropseq data. Is it possible to just plug the dgTMatrix to estimate Soup?

Best, Yolanda

constantAmateur commented 5 years ago

Hi Yolanda,

All that SoupX needs to work is a sparse matrix containing counts for each gene from all droplets generated in the experiment (including empty ones) and a vector indicating which of these droplets contain cells. If the dgTMatrix you provide meets these criteria there is no reason it shouldn't work. Have a look at the help for SoupChannel for details of how to load the data.