<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>

CC BY-SA 4.0
2018-05-25T12:16:44.313Z
2018-05-25T12:16:44.313Z
Kasper Thystrup Karstensen
<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>

CC BY-SA 4.0
2018-05-26T12:21:10.740Z
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)
Alon Gelber
<scrnaseq><10x-genomics>
Raw vs Filtered in the output of cellranger count
# 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)  

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## 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)


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