scRNA analysis in PDX model
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3 months ago

Hi I'm doing single cell RNA analysis in PDX model and I want to separate my data into mouse and human cell before start analyzing, anyone knows how to do this in R using subset function or any other possible ways?

NGS PDX scRNA • 293 views
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At what point in the analysis are you starting from, and what files do you currently have?

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I used cellranger chimeric reference to align data and loaded filtered_feature_bc_matrix into matrix. I used following scripts.

barcode.path <- paste0(matrix_dir, "barcodes.tsv.gz")

features.path <- paste0(matrix_dir, "features.tsv.gz")

matrix.path <- paste0(matrix_dir, "matrix.mtx.gz")

mat <- readMM(file=matrix.path)

feature.names = read.delim(features.path,
                            header=FALSE,
                            stringsAsFactors = FALSE)

barcode.names = read.delim(barcode.path,
                           header= FALSE,
                           stringsAsFactors = FALSE)

colnames(mat) = barcode.names$V1

Then I tried to separate human and mouse by colnames, though not sure if it was appropriate to use c1 to represent first column

human <- subset(normal, c1= "GRCh38-*")

mouse <- subset(normal, c1= "mm10-*")

This didn't work at all. Thansk ! Any experts can help me out?

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I tried to use a tool called "xenocell" but I was not familiar with docker

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