What count matrix should be used with SoupX?

constantAmateur / SoupX

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

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What count matrix should be used with SoupX? #62

Closed tkapello closed 3 years ago

tkapello commented 3 years ago

Hi,

thanks for this useful tool, I want to try it on my dataset. I have a Seurat object an want to remove background noise to improve my clustering. Which count table would you recommend? Raw or normalized counts? And, if I understand correctly the vignette, one can continue downstream analysis with the output?

Thanks in advance!

constantAmateur commented 3 years ago

You must input raw count matricies. Ideally you should start from the cellranger output folder for 10X data. This is because the empty droplets are used to calculate the composition of the contamination.

The results of adjustCounts can be used as input for Seurat or any other analysis. The vignette has more details.