<p>It is been a while since the last time I have done this, but the problem seems to be your filenames. For example <code>Read10X()</code> is expecting a file <code>barcodes.tsv.gz</code> but you seem to have sample prefixes in your file names <code>GSM7494257_AML16_DX_raw_barcodes.tsv.gz</code>.</p>
<p>If I remember correctly, <code>cellranger</code> outputs a directory sth like <code>sample-name/outs/</code> and this <code>outs</code> dir contains <code>barcodes.tsv.gz</code>, <code>genes.tsv.gz</code>, <code>matrix.mtx.gz</code> that <code>Seurat</code> can easily read.</p>

CC BY-SA 4.0
2024-04-09T00:52:30.283Z
Thank you much, you are right! Exactly the name without prefixes.
Kent Yang
CC BY-SA 4.0
2024-04-07T07:26:44.063Z
2024-04-07T07:26:44.063Z
haci
<p>I am loading cellranger data into seuratobject as following, but it keeps showing Error in</p>
<pre><code>Barcode file missing. Expecting barcodes.tsv.gz
</code></pre>
<p>the running code and result:</p>
<pre class="lang-r prettyprint-override"><code>#clean up your environment
rm(list=ls())

# Load required libraries
library(Seurat)
library(dplyr)

# Load required library for reading Matrix Market files
library(Matrix)

# For output from CellRanger &gt;= 3.0 with multiple data types
data_dir &lt;- 'C:/Users/Administrator/Desktop/10x_raw'

list.files(data_dir) # Should show barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz
[1] &quot;GSM7494257_AML16_DX_raw_barcodes.tsv.gz&quot; &quot;GSM7494257_AML16_DX_raw_genes.tsv.gz&quot;   
[3] &quot;GSM7494257_AML16_DX_raw_matrix.mtx.gz&quot;  

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

seurat_object = CreateSeuratObject(counts = data<span class="math-container">$`Gene Expression`)
Error in data$</span>`Gene Expression` : 
  object of type 'closure' is not subsettable
</code></pre>
<p>I am sure this file inside the directory. Dose anyone know what's the issue?</p>
<p>Thanks in advance.</p>

CC BY-SA 4.0
2024-04-07T12:04:45.550Z
The `list.files` line demonstrates that the precise files it's looking for are not there. What do you mean by "I am sure this file inside the directory"? Can you show a listing of files in the directory that you are trying to read from?
gringer
<scrnaseq><seurat><cellranger>
How to import data from cell ranger to R (Seurat) using Read10X?
# How to import data from cell ranger to R (Seurat) using Read10X?

(Asked by: username_0 on 2024-04-06)

I am loading cellranger data into seuratobject as following, but it keeps showing Error in
Barcode file missing. Expecting barcodes.tsv.gz

the running code and result:
#clean up your environment
rm(list=ls())

# Load required libraries
library(Seurat)
library(dplyr)

# Load required library for reading Matrix Market files
library(Matrix)

# For output from CellRanger >= 3.0 with multiple data types
data_dir <- 'C:/Users/Administrator/Desktop/10x_raw'

list.files(data_dir) # Should show barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz
[1] "GSM7494257_AML16_DX_raw_barcodes.tsv.gz" "GSM7494257_AML16_DX_raw_genes.tsv.gz"   
[3] "GSM7494257_AML16_DX_raw_matrix.mtx.gz"  

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

seurat_object = CreateSeuratObject(counts = data$`Gene Expression`)
Error in data$`Gene Expression` : 
  object of type 'closure' is not subsettable

I am sure this file inside the directory. Dose anyone know what's the issue?
Thanks in advance.

**Tags:** scrnaseq, seurat, cellranger
> **Comments:**
> **username_1**: The `list.files` line demonstrates that the precise files it's looking for are not there. What do you mean by "I am sure this file inside the directory"? Can you show a listing of files in the directory that you are trying to read from?  

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## 1 answers

### Answer by username_2 on 2024-04-07. Score: 1

It is been a while since the last time I have done this, but the problem seems to be your filenames. For example `Read10X()` is expecting a file `barcodes.tsv.gz` but you seem to have sample prefixes in your file names `GSM7494257_AML16_DX_raw_barcodes.tsv.gz`.

If I remember correctly, `cellranger` outputs a directory sth like `sample-name/outs/` and this `outs` dir contains `barcodes.tsv.gz`, `genes.tsv.gz`, `matrix.mtx.gz` that `Seurat` can easily read.

> **Comments:**
> **username_0**: Thank you much, you are right! Exactly the name without prefixes.  

---

