Using SoupX for indrops data (non 10x genomics output)

[JoyOtten]

Dear all,

I wanted to ask if we could use SoupX on data that is not delivered or run by 10x genomics. The problem that I have so far is that I don't have the filtered gene matrix, but I do have the raw gene matrix. I'm wondering if it's possible to create the filtered gene matrix yourself or run apart from the cellranger pipeline.

Thank you, Joy

[nouhaylaeraysy]

Hello, I started with SoupX me too i have the same problem did you manage to solve it? please if you have an idea response me. Thank you in advance.

[JoyOtten]

Hi, I was able to construct a Seurat Object with the following lines of code if you're using R:

seurat <- CreateSeuratObject(counts, project = "name1", assay = "RNA", min.cells = 0, min.features = 0, names.field = 1, names.delim = "_", meta.data = metadata)

Basically I filtered the counts beforehand and then made a seurat object and put it into SoupX

[nouhaylaeraysy]

Hello, thank you for your response , actually I'm working with 3 libraries i want to apply soupx then integrate them , this is my code : ib1 <- readRDS("lib1_NoDoublet.rds") lib2 <- readRDS("lib2_NoDoublet.rds") lib3 <- readRDS("lib3_NoDoublet.rds") reference_list <- c(lib1,lib2, lib3) reference_list

lib1@meta.data

this is what i have in metadata of lib1 : orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 seurat_clusters AAACCCAAGACAGTCG-1 Lib1 1657 738 2 2 AAACCCAAGGTTCACT-1 Lib1 6227 2015 7 7 AAACCCACAACCAGAG-1 Lib1 844 463
0 0

pANN_0.25_0.3_951 DF.classifications_0.25_0.3_951 AAACCCAAGACAGTCG-1 0.08571429 Singlet AAACCCAAGGTTCACT-1 0.35801394 Singlet

can you tell me how i can apply soupx for the 3 libraries? Thank you again. Best

[JoyOtten]

Hi you need to apply SoupX separately for each library. Please read the paper accordingly and this might help you along. https://rawcdn.githack.com/constantAmateur/SoupX/204b602418df12e9fdb4b68775a8b486c6504fe4/inst/doc/pbmcTutorial.html

[nouhaylaeraysy]

Hi Thank you , i have just a filtred_features_bc_matrix i don't have a raw_feature_bc_matrix , so how i can find tod ?because in this paper they have 2 data : toc = Seurat::Read10X(file.path(tmpDir, "filtered_gene_bc_matrices", "GRCh38")) tod = Seurat::Read10X(file.path(tmpDir, "raw_gene_bc_matrices", "GRCh38"))