Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-16T11:35:51.537Z
Answers.LastActivityDate: 2017-06-16T14:26:03.450Z
Answers.LastEditDate: 2017-06-16T14:26:03.450Z
Answers.UserDisplayName: Peter
Body: <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>
  
Tags: <rna-seq><r><bioconductor><scrnaseq><10x-genomics>
Title: 10x Genomics Chromium single-cell RNA-seq data analysis options?
ThreadText: # 10x Genomics Chromium single-cell RNA-seq data analysis options?
  
  (Asked by: username_0 on 2017-06-16)
  
  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?
  
  **Tags:** rna-seq, r, bioconductor, scrnaseq, 10x-genomics
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2017-06-16. Score: 4 | Accepted answer
  
  # Data preparation
  
  Cell Ranger uses the Illumina sequencing output (`.bcl`) files
  
  1. [Make fastq files](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq):
     `cellranger mkfastq` ==> `.fastq`
  2. Prepare count matrix: `cellranger count` ==> `matrix.mtx, web_summary.html, cloupe.cloupe`
  3. Optional: combine multiple `matrix.mtx` files (libraries): `cellranger aggr`
  
  ---
  
  # Data analysis
  
  **[Loupe Cell Browser](https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser) visualization of** `cloupe.cloupe` **files**
  
  **Count table** `matrix.mtx` **analysis options:**
  
  * [`Python`](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/python)
  * `R` [Cell Ranger R Kit](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/rkit): `cellrangerRkit::load_cellranger_matrix()` ==> ExpressionSet
  * `R` [Scater](http://hemberg-lab.github.io/scRNA.seq.course/scater-package.html): `scater::read10XResults()` ==> SCESet object
  * `R` [Seurat](http://satijalab.org/seurat/pbmc-tutorial.html): `Seurat::Read10X()` ==> Seurat object
  
  
  ---
  
  