Error in Read10X(data.dir

Question

[yang.zhizhang]

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.

Answer 1

[antonioggsousa]

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

[yang.zhizhang]

You are absolutely right. Thanks so much.

[bioinformatics]

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

[antonioggsousa]

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

[Sophie]

I'm getting the same error code. What commands do you use to decompress the tar.gz file? Thank you

[antonioggsousa]

It depends on the operating system (OS) that you're running.

If you want to decompress a .tar.gz folder outside R, see the following guide depending on your OS: https://kinsta.com/knowledgebase/unzip-tar-gz/. If you're using Linux, you can do the following in your terminal: tar -xvzf folder.tar.gz (where folder.tar.gz represents the folder that you want to decompress)

If you want to do it from R directly for convenience, you can attempt the following - see the youtube video (I never try it myself but it seems straightforward): https://www.youtube.com/watch?v=-7s03AzEvag. The solution relies on the function untar(). It seems that you only need to provide the .tar.gz folder as input like this: untar("folder.tar.gz").

I hope this helps.

António