Answers.Body: <p>I'm unsure whether this is the answer you are looking for, but when looking into 10X cellranger documentation for the Matrices Output:</p>
  
  <blockquote>
    <p><strong>Unfiltered gene-barcode matrices</strong>:
    <em>Contains every barcode from fixed list of known-good barcode sequences. This includes background and non-cellular barcodes.</em></p>
    
    <p><strong>Filtered gene-barcode matrices</strong>:
    <em>Contains only detected cellular barcodes.</em></p>
  </blockquote>
  
  <p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices" rel="noreferrer">Source</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-25T12:16:44.313Z
Answers.LastActivityDate: 2018-05-25T12:16:44.313Z
Answers.UserDisplayName: Kasper Thystrup Karstensen
Body: <p>After running <code>cellranger count</code> I got two relevant for further analysis folders: <code>filtered_gene_bc_matrices</code> and <code>raw_gene_bc_matrices</code>. What is the difference between them? What does <code>cellranger</code> filter out, and what should we preferably use for further analysis?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-26T12:21:10.740Z
Comments.Text: Mostly people use the filtered gene bc matrix. Take a look at the guided tutorial for the r package Seurat if you're new to 10x and /or single cell (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Comments.UserDisplayName: Alon Gelber
Tags: <scrnaseq><10x-genomics>
Title: Raw vs Filtered in the output of cellranger count
ThreadText: # Raw vs Filtered in the output of cellranger count
  
  (Asked by: username_0 on 2018-05-24)
  
  After running `cellranger count` I got two relevant for further analysis folders: `filtered_gene_bc_matrices` and `raw_gene_bc_matrices`. What is the difference between them? What does `cellranger` filter out, and what should we preferably use for further analysis?
  
  **Tags:** scrnaseq, 10x-genomics
  
  > **Comments:**
  > **username_1**: Mostly people use the filtered gene bc matrix. Take a look at the guided tutorial for the r package Seurat if you're new to 10x and /or single cell (https://satijalab.org/seurat/pbmc3k_tutorial.html)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-05-25. Score: 5 | Accepted answer
  
  I'm unsure whether this is the answer you are looking for, but when looking into 10X cellranger documentation for the Matrices Output:
  
  > **Unfiltered gene-barcode matrices**:
  > *Contains every barcode from fixed list of known-good barcode sequences. This includes background and non-cellular barcodes.*
  >
  > **Filtered gene-barcode matrices**:
  > *Contains only detected cellular barcodes.*
  
  [Source](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices)
  
  
  ---
  
  