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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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Loading data and downstream steps #52

Closed Nur-Taz closed 4 years ago

Nur-Taz commented 4 years ago

Hi @constantAmateur: I am having troubling loading my dataset with load10x for the top level cellranger output.

(1) I can do SoupChannel with tod and toc. But the next step is estimateSoup or setSoupProfile, right? After which I have to add the metadata, such as the clustering, correct?

(2) When loading tod and toc using Seurat::Read10X, what is the purpose of saying "GRCh38"? (on the vignette).

(3) For setclusters to work if I can't upload the cellranger outs folder, I have to put my own clustering info. Is that clustering done on the raw_feature_bc_matrix, for example, using Seurat? Or does it have to be done on both raw and filtered bc matrix?

Thanks a lot for your response, and any additional information that you think will help me. For my dataset, I want to get to a point where I can use autoEstCont.

Nur-Taz commented 4 years ago

I solved all the issues I was having, so I'll close the issue. If anyone drops by this issue, and are interested in learning about the solutions, feel free post and tag me, and I will be happy to share my findings.

hothri commented 3 years ago

@Nur-Taz Hi, Which information have you used for clustering?