Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-09T00:52:30.283Z
Answers.Text: Thank you much, you are right! Exactly the name without prefixes.
Answers.UserDisplayName: Kent Yang
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-07T07:26:44.063Z
Answers.LastActivityDate: 2024-04-07T07:26:44.063Z
Answers.UserDisplayName: haci
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-07T12:04:45.550Z
Comments.Text: 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?
Comments.UserDisplayName: gringer
Tags: <scrnaseq><seurat><cellranger>
Title: How to import data from cell ranger to R (Seurat) using Read10X?
ThreadText: # 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:
  
  ```r
  #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?  
  
  ---
  
  ## 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.  
  
  ---
  
  