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7 weeks ago

Hi, I am new to R and recently want to replicate a R demo with Seurat. The dataset is downloaded into my PC hard driver with the file name of "pbmc3k_filtered_gene_bc_matrices.tar.gz". I successfully loaded packages of dplyr, Seurat, patchwork which are required to run the code. Then, I tried to load dataset using code: pbmc.data<-Read10X(data.dir="~/R/10x/pbmc3k_filtered_gene_bc_matrices.tar.gz/") and get message "Error in Read10X(data.dir = "~/R/10x/pbmc3k_filtered_gene_bc_matrices.tar.gz/") : Directory provided does not exist. I have changed directory path and get the same error message. Please help. Thanks so much.

Seurat • 522 views
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7 weeks ago
antonioggsousa ★ 2.4k

Hi,

The files that you downloaded are tar.gz compressed (this can be decompressed in the command-line or using GUI programs - some OS like ubuntu can decompress it without any problem). Please decompress the files first and only then provide the path to the folder filtered_gene_bc_matrices/hg19/ like the tutorial mentions:

pbmc.data <- Read10X(data.dir = "../data/pbmc3k/filtered_gene_bc_matrices/hg19/")


Right now you're saying to import the files under the compressed folder:

"~/R/10x/pbmc3k_filtered_gene_bc_matrices.tar.gz/"


Which of course do not exist (Directory provided does not exist) because the software can not read anything under the compressed folder.

I hope this helps,

António

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You are absolutely right. Thanks so much.

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I also have the same problem. I have tried to load the dataset using code: data <- Read10X(data.dir = "GSE162454_RAW"). I received an message error Directory provided does not exist Do you know where I've gone wrong? In the folder is 3 files: features, matrix and barcodes.

Thankyou

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Perhaps you are not giving the full path to the folder. I'm not sure, but your problem seems to be different since your GSE162454_RAW folder is decompressed. Type the command in R list.files("GSE162454_RAW") to see if you can list the files from the directory where you are trying to import this. If you can list, I cannot figure out the problem. If you can't, it means that the path that you're giving is wrong.

António