sci-RNA-seq
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Entering edit mode
15 days ago
kilcdincer ▴ 10

Hello,

I have sci-RNA-seq data. I applied standart Seuat pipeline. However, I have ‘dirty’ clusters on UMAP. So some clusters are mixed. What can I do to solve it? Can I use doublet removers for sci-RNA-seq data?

library(Seurat)

# Load the control dataset
ctrl.data <- Read10X(data.dir = "ctrl//")

# Initialize the Seurat object
ctrl <- CreateSeuratObject(counts = ctrl.data, project = "control", min.cells = 3, min.features = 200)

# filtering
ctrl <- subset(ctrl, subset = nFeature_RNA > 100 & nFeature_RNA < 5000)

# Normalizing the data
ctrl <- NormalizeData(ctrl, normalization.method = "LogNormalize", scale.factor = 10000)

# Identification of highly variable features (feature selection) 
ctrl <- FindVariableFeatures(ctrl, selection.method = "vst", nfeatures = 2000)

# Scaling the data 
ctrl <- ScaleData(ctrl)

# Perform linear dimensional reduction 
ctrl <- RunPCA(ctrl)

# Determine the ‘dimensionality’ of the dataset 
ElbowPlot(ctrl)

# Cluster cells
ctrl <- FindNeighbors(ctrl, dims = 1:15)
ctrl <- FindClusters(ctrl, resolution = c(0.3, 0.5, 0.7))

ctrl <- SetIdent(ctrl, value = "RNA_snn_res.0.7")

# Run non-linear dimensional reduction
ctrl <- RunUMAP(ctrl, dims = 1:15)

DimPlot(ctrl, reduction = "umap", label = T)

here is the clustering plot

Seurat sci-RNA-seq • 165 views
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Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it makes noise..." => no mechanic can solve that with this description.

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