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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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Isssue of 'toc' and tod" #106

Closed kathywawa closed 2 years ago

kathywawa commented 2 years ago

Hi, Professors, I have some questions to ask you. First, what files do I need to prepare for analyzing SoupX. Next, how can I set up toc and tod when I analyze my own single-cell sequencing data. Thanks. kathy

constantAmateur commented 2 years ago

toc is short for table of cells and should include only those barcodes that contain cells (e.g. the filtered counts folder in the cellranger output). tod is short for table of droplets and should include all barcodes (e.g. the raw counts folder in the cellranger output).