Using SoupX for indrops data (non 10x genomics output)
JoyOtten opened this issue · 5 comments
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
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.
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
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
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
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
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"))