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I am trying to follow the Seurat tutorial found here: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

The PBMC raw data from the tutorial downloads to my computer as: pbmc3k_filtered_gene_bc_matrices.tar.gz

I am having trouble uploading the PBMC raw data into R. According to the tutorial, the code ought to be

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

This makes no sense to me, as the name of the data file does not match the data directory. Here is what I tried in order to upload (which does not work):

setwd("C:/Users/myname/Downloads")
pbmc.raw.data <- gzfile("pbmc3k_filtered_gene_bc_matrices.tar.gz")
pbmc.data <- Read10X(pbmc.raw.data)

Any suggestions would be appreciated how to upload the data so I may complete the tutorial. Thanks in advance!

Lucia Wagner
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    The `.tar.gz` file is an archive. You need to extract the files and directories therein. You did not say what operating system you are using. If you are on Linux, you can use `tar xf pbmc3k_filtered_gene_bc_matrices.tar.gz` on the command line. – Mark Adler Jul 09 '22 at 13:58
  • Thank you @MarkAdler ! This was useful. I am using Windows, and I figured out how to unzip the file using the command system. – Lucia Wagner Jul 12 '22 at 15:43

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