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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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Estimating and adjusting counts in soupx #46

Closed rubinaasharmaa closed 4 years ago

rubinaasharmaa commented 4 years ago

Hi, I need to clean my scRNA seq data. I tried following the soupx vignette. But not able to estimate and adjust counts in soupx after loading10X files (both raw and filtered). It gives the following error:

"Error in autoEstCont(sc) : Clustering information must be supplied, run setClusters first."

I will appreciate your help. Thanks in advance.

constantAmateur commented 4 years ago

As the error says, you need to provide clustering information for the auto estimation procedure to work. Clustering information is recommended even if you are not using this function.

If you are using 10X data mapped with cellranger, this should be loaded from the analysis folder by load10X. Otherwise you will have to cluster your data using some method (e.g. Seurat) and then set it first using setClusters.

rubinaasharmaa commented 4 years ago

HI,

I am kind of beginner in R. Ok. I know how to create clusters in seurat but how can i later use it as set clusters in soupx. Can you please explain a bit ? I will highly appreciate your help and guidance.

Thanks, Rubina Sharma

On Mon, May 18, 2020 at 9:59 AM Matthew D. Young notifications@github.com wrote:

As the error says, you need to provide clustering information for the auto estimation procedure to work. Clustering information is recommended even if you are not using this function.

If you are using 10X data mapped with cellranger, this should be loaded from the analysis folder by load10X. Otherwise you will have to cluster your data using some method (e.g. Seurat) and then set it first using setClusters.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/constantAmateur/SoupX/issues/46#issuecomment-630201373, or unsubscribe https://github.com/notifications/unsubscribe-auth/APTE5GVBATFFYT2UIR67ICDRSE5LBANCNFSM4NDAXQIA .

-- Regards Rubina Sharma, Ph.D. Post doctoral fellow NIDCR, NIH Bldg 30, Rm 303 30 Convent Drive Bethesda, MD 20892, USA

https://scholar.google.co.in/citations?user=Kf_73ckAAAAJ&hl=en

constantAmateur commented 4 years ago

If you created a Seurat object using srat = CreateSeuratObject(sc$toc) then after normal processing to call clusters you need only run sc = setClusters(sc,srat@active.ident)

ChintanChhatbar commented 2 years ago

Hi Matthew, Thanks for the nice package. If i run soupX on a seurat object as said above, can i run it on a combined object? Best, Chintan