satijalab / seurat

R toolkit for single cell genomics

http://www.satijalab.org/seurat

Other

2.24k stars 902 forks source link

Raw data is tar.gz. Error message: "Expecting barcodes.tsv.gz" #4352

Closed algebio closed 3 years ago

algebio commented 3 years ago

Hello

I am trying to run this pipeline: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html.

I have downloaded the raw data (which is a .tar.gz file) from the link in the first paragraph "The raw data can be found here."

When I run the line:

Load the PBMC dataset

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

I get the error: Error in Read10X(data.dir = "C:/Users/njo47/OneDrive - Newcastle University/Documents/Seurat/clustering") : Barcode file missing. Expecting barcodes.tsv.gz

Am I doing something wrong?

Thank you for your help.

samuel-marsh commented 3 years ago

Hi,

Not member of dev team but hopefully can be helpful. Are the barcodes, genes, and matrix files found at the file path: "C:/Users/njo47/OneDrive - Newcastle University/Documents/Seurat/clustering"? Can you also post what version of Seurat you are running? I'm able to load the files without issue.

Best, Sam

algebio commented 3 years ago

Hi Sam

I only get one .tar.gz file when I click the link "here" in the first paragraph in https://satijalab.org/seurat/articles/pbmc3k_tutorial.html. The file is in the correct path. Seurat version is 4.0.0

How many files do you get from that same link?

Thank you for help. Regards Juan

samuel-marsh commented 3 years ago

Hi Juan,

That is zipped archive. You need to unzip the download before supply path to Read10X.

Best, Sam

algebio commented 3 years ago

My god! How much I have to learn.....

Thank you Sam.

samuel-marsh commented 3 years ago

No problem! happy to help!