why do I get this error while reading single cell RNA seq data in R

Question

[nuorain]

Hi, I got this error. Why? I appreciate your help. Thank you very much.

Error in Read10X(data.dir = data_dir) : 
  Barcode file missing. Expecting barcodes.tsv.gz

list.files(data_dir)
 [1] "GSM5004180_PT1_barcodes.tsv.gz" "GSM5004180_PT1_features.tsv.gz"
 [3] "GSM5004180_PT1_matrix.mtx.gz"   "GSM5004181_PT2_barcodes.tsv.gz"

cyto<- Read10X(data.dir = data_dir) 
Error in Read10X(data.dir = data_dir) : 
  Barcode file missing. Expecting barcodes.tsv.gz

[GenoMax]

It is often useful to do a quick search with the error. Here is one of the first search results that explains the issue: https://github.com/satijalab/seurat/issues/1625 . YOu also have more than one sample in this folder.

Answer 1

[ATpoint]

What GenoMax links. These functions assume that files are called matrix.mtx.gt, barcodes.tsv.gz and genes.tsv.gz. That means, with multiple samples you need to create separate folders, with one set of files each.

[nuorain]

Hi, ATpoint. How to name the separate folders for each sample? Thanks.

[GenoMax]

You can name the folders using sample names e.g. GSM5004180_PT1. Then rename the files for that samples to what ATpoint showed above and place inside each sample directory.

[nuorain]

Thanks GenoMax. So one sample has three files. I don't have problem with inputting one sample under one directory. But I have trouble with reading multiple samples at the same time. Do you have any scripts which can overcome this problem? Thank you very much again.