text: user208: Provide an overview of 10x data analysis packages.
  10x provides Cell Ranger which prepares a count matrix from the bcl sequencer output files and other files (see bottom of page https://support.10xgenomics.com/docs/license for the programs it uses).
  What can we do with the output files?
  
  user208: Data preparation
  Cell Ranger uses the Illumina sequencing output (.bcl) files
  
  Make fastq files:
  cellranger mkfastq ==> .fastq
  Prepare count matrix: cellranger count ==> matrix.mtx, web_summary.html, cloupe.cloupe
  Optional: combine multiple matrix.mtx files (libraries): cellranger aggr
  
  
  Data analysis
  Loupe Cell Browser visualization of cloupe.cloupe files
  Count table matrix.mtx analysis options:
  
  Python
  R Cell Ranger R Kit: cellrangerRkit::load_cellranger_matrix() ==> ExpressionSet
  R Scater: scater::read10XResults() ==> SCESet object
  R Seurat: Seurat::Read10X() ==> Seurat object
  
  
original_text: 208: <p>Provide an overview of 10x data analysis packages.</p>
  
  <p>10x provides Cell Ranger which prepares a count matrix from the bcl sequencer output files and other files (see bottom of page <a href="https://support.10xgenomics.com/docs/license" rel="nofollow noreferrer">https://support.10xgenomics.com/docs/license</a> for the programs it uses).</p>
  
  <p>What can we do with the output files?</p>
   208: <h1>Data preparation</h1>
  
  <p>Cell Ranger uses the Illumina sequencing output (<code>.bcl</code>) files</p>
  
  <ol>
  <li><p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq" rel="nofollow noreferrer">Make fastq files</a>:
  <code>cellranger mkfastq</code> ==> <code>.fastq</code></p></li>
  <li><p>Prepare count matrix: <code>cellranger count</code> ==> <code>matrix.mtx, web_summary.html, cloupe.cloupe</code></p></li>
  <li>Optional: combine multiple <code>matrix.mtx</code> files (libraries): <code>cellranger aggr</code></li>
  </ol>
  
  <hr>
  
  <h1>Data analysis</h1>
  
  <p><strong><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser" rel="nofollow noreferrer">Loupe Cell Browser</a> visualization of</strong> <code>cloupe.cloupe</code> <strong>files</strong></p>
  
  <p><strong>Count table</strong> <code>matrix.mtx</code> <strong>analysis options:</strong></p>
  
  <ul>
  <li><p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/python" rel="nofollow noreferrer"><code>Python</code></a></p></li>
  <li><p><code>R</code> <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/rkit" rel="nofollow noreferrer">Cell Ranger R Kit</a>: <code>cellrangerRkit::load_cellranger_matrix()</code> ==> ExpressionSet</p></li>
  <li><p><code>R</code> <a href="http://hemberg-lab.github.io/scRNA.seq.course/scater-package.html" rel="nofollow noreferrer">Scater</a>: <code>scater::read10XResults()</code> ==> SCESet object</p></li>
  <li><p><code>R</code> <a href="http://satijalab.org/seurat/pbmc-tutorial.html" rel="nofollow noreferrer">Seurat</a>: <code>Seurat::Read10X()</code> ==> Seurat object</p></li>
  </ul>
  