Unable to read single cell dataset from GEO

Question

[wshin765]

I'm fairly new to using Seurat and R in general. I downloaded this dataset from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122703) and tried running it with this code after unzipping the file:

ctcl.data <- Read10X(data.dir = "/Users/NAME/Desktop/scrnaseq/GSE122703_RAW/")

The error it gives me is:

Error in Read10X(data.dir = "/Users/NAME/Desktop/scrnaseq/GSE122703_RAW/") : Barcode file missing. Expecting barcodes.tsv.gz

Am I suppose to rename each file to something else? I unzipped each of the files (barcodes, genes, matrix) but it still gives me this error. The Seurat I am running on is v4.1.0, and the Seurat from the paper is v2.3.4

Answer 1

[Soheil]

This dataset contains two different samples; GSM3478791 and GSM3478792. Each sample should be in a separate folder. Also if you look at Read10X source code you will see what files it looks for.

After extracting and copying the samples into different folders rename them as follows:

GSM3478791_P4_barcodes.tsv.gz ---> barcodes.tsv.gz

GSM3478791_P4_genes.tsv.gz ---> features.tsv.gz

GSM3478791_P4_matrix.mtx.gz ---> matrix.mtx.gz

Hope this helps!

[wshin765]

Thank you!