text: user2005: 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?
  
  user2153: 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
  
original_text: 2005: <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>
   2153: <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>
  