Estimated global contamination fraction and cluster info

constantAmateur / SoupX

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

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Estimated global contamination fraction and cluster info #38

Closed jmzvillarreal closed 4 years ago

jmzvillarreal commented 4 years ago

Hi, I think I don't fully understand what Estimated global contamination fraction represents ¿the average conatmination fraction per droplet? How would cluster information more accurately get rid of contamination ? Thanks, Jaime.

constantAmateur commented 4 years ago

Please refer to our manuscript that discusses the implementation in detail https://www.biorxiv.org/content/10.1101/303727v2

The global contamination fraction is the average fraction of molecules expected to be ambient RNA derived in each droplet. To understand how clustering allows more accurate contamination removal please refer to the paper.