Answers.Body: <p>You can follow the <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices" rel="nofollow noreferrer">10X instructions</a> to load your matrix into R:
  the following is a direct quote from their webpage: </p>
  
  <blockquote>
  <pre><code>library(Matrix)
  matrix_dir = "/opt/sample345/outs/filtered_feature_bc_matrix/"
  barcode.path &lt;- paste0(matrix_dir, "barcodes.tsv.gz")
  features.path &lt;- paste0(matrix_dir, "features.tsv.gz")
  matrix.path &lt;- paste0(matrix_dir, "matrix.mtx.gz")
  mat &lt;- readMM(file = matrix.path)
  feature.names = read.delim(features.path, 
                             header = FALSE,
                             stringsAsFactors = FALSE)
  barcode.names = read.delim(barcode.path, 
                             header = FALSE,
                             stringsAsFactors = FALSE)
  colnames(mat) = barcode.names<span class="math-container">$V1
  rownames(mat) = feature.names$</span>V1
  </code></pre>
  </blockquote>
  
  <p>You can then create a seurat object using mat</p>
  
  <pre><code>object &lt;- CreateSeuratObject(mat, project="")
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-15T21:39:40.757Z
Answers.LastActivityDate: 2019-08-15T21:39:40.757Z
Answers.UserDisplayName: Mack123456
Body: <p>it is said that the features.tsv from Cell Ranger v3 is analogous to the genes.tsv from Cell Ranger v2. So can I change the file name to genes.tsv for Seurat to read it? I know that Seurat has the update version 3 that can read the features.tsv, and I would like to use the old version. So if I change the file name, did it cause any problem?<a href="https://i.sstatic.net/pRplq.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/pRplq.png" alt="enter image description here"></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-15T21:05:52.490Z
Comments.Text: You can find an answer here: https://github.com/satijalab/seurat/issues/1196. In brief: Read10X is convenience, you can use the files yourself to generate the matrix but if you only have RNA in your experiment your strategy should work. Did you unzip the file and rename? or rename the zipped file?
Comments.UserDisplayName: Mack123456
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-15T21:47:37.890Z
Comments.Text: Thank you for your reply, and I unzip the file and rename it. Much appreciated!
Comments.UserDisplayName: hua
Tags: <single-cell>
Title: Can I change the name of file features.tsv to genes.tsv
ThreadText: # Can I change the name of file features.tsv to genes.tsv
  
  (Asked by: username_0 on 2019-08-15)
  
  it is said that the features.tsv from Cell Ranger v3 is analogous to the genes.tsv from Cell Ranger v2. So can I change the file name to genes.tsv for Seurat to read it? I know that Seurat has the update version 3 that can read the features.tsv, and I would like to use the old version. So if I change the file name, did it cause any problem?[![enter image description here](https://i.sstatic.net/pRplq.png)](https://i.sstatic.net/pRplq.png)
  
  **Tags:** single-cell
  
  > **Comments:**
  > **username_1**: You can find an answer here: https://github.com/satijalab/seurat/issues/1196. In brief: Read10X is convenience, you can use the files yourself to generate the matrix but if you only have RNA in your experiment your strategy should work. Did you unzip the file and rename? or rename the zipped file?  
  > **username_0**: Thank you for your reply, and I unzip the file and rename it. Much appreciated!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-08-15. Score: 1
  
  You can follow the [10X instructions](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices) to load your matrix into R:
  the following is a direct quote from their webpage:
  
  > ```
  > library(Matrix)
  > matrix_dir = "/opt/sample345/outs/filtered_feature_bc_matrix/"
  > barcode.path <- paste0(matrix_dir, "barcodes.tsv.gz")
  > features.path <- paste0(matrix_dir, "features.tsv.gz")
  > matrix.path <- paste0(matrix_dir, "matrix.mtx.gz")
  > mat <- readMM(file = matrix.path)
  > feature.names = read.delim(features.path, 
  >                            header = FALSE,
  >                            stringsAsFactors = FALSE)
  > barcode.names = read.delim(barcode.path, 
  >                            header = FALSE,
  >                            stringsAsFactors = FALSE)
  > colnames(mat) = barcode.names$V1
  > rownames(mat) = feature.names$V1
  >
  > ```
  
  You can then create a seurat object using mat
  
  ```
  object <- CreateSeuratObject(mat, project="")
  
  ```
  
  
  ---
  
  