Answers.Body: <p>I wrote a simple script to do it. Not sure whether that's what you want.</p>
  <pre><code>#!/bin/bash
  #CellrangerSummary.sh Sample1 Sample2
  csvtool transpose <span class="math-container">$1/outs/*summary.csv | csvcut -c 1 &gt; summary.csv
  for sample in "$</span>@&quot;
      do
          csvtool transpose <span class="math-container">$sample/outs/*summary.csv &gt; tempfilesforcsvtool.$</span>sample
          csvjoin -c 1 summary.csv tempfilesforcsvtool.<span class="math-container">$sample &gt; temp2
      mv temp2 summary.csv
  rm tempfilesforcsvtool.$</span>sample
      done
  
  csvformat -T summary.csv &gt; summary.tsv
  rm summary.csv
  <span class="math-container">```</span>
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-21T19:41:00.850Z
Answers.LastActivityDate: 2021-03-22T22:53:48.450Z
Answers.LastEditDate: 2021-03-22T22:53:48.450Z
Answers.UserDisplayName: Code42
Body: <p>I have a number of single-cell projects processed with <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger" rel="noreferrer">cellranger from 10x Genomics</a>. The pipeline produces a number of handy metrics that are summarized for each Illumina sample in <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/summary" rel="noreferrer">web page</a>. These include things like the estimated number of cells, the fraction of reads in cells, and mapping rates. What I would like is to aggregate this information from multiple Illumina samples into a single file. <a href="http://multiqc.info/" rel="noreferrer">MultiQC</a> is the obvious choice for such a task, but it appears that no one has written a module to process cellranger data for it. Are there any other prepackaged ways to perform this aggregation?</p>
  
  <p>If there's no convenient tool for this I'll just write a MultiQC module, but I'd obviously like to avoid the extra effort unless it's really needed.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-01T20:57:51.423Z
Comments.Text: Single-cell RNA-seq analysis is still developing (not crystallized yet), so I think what you want is not there yet. If you think it may be handy for your analysis, many more may follow, so making a tool for this might be fruitful (if you make it available for others).
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-11T15:57:38.897Z
Comments.Text: We’ve written a MultiQC module for Supernova, but not Long ranger or Cell Ranger (yet). I agree that one would be useful, and probably quite quick to write if there’s also a JSON summary file output for that tool too. We’ve been talking about this recently. Did you ever get anywhere with writing a new module?
Comments.UserDisplayName: ewels
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-16T09:59:08.877Z
Comments.Text: any new about that? The cellranger is now version 5 and produce still data that would be great to compile in a single report.
Comments.UserDisplayName: Gildas
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-16T20:19:02.033Z
Comments.Text: Things move fast.  Cellranger now has a version 6.0
Comments.UserDisplayName: swbarnes2
Tags: <scrnaseq><cellranger>
Title: Aggregate sequencing/mapping/etc. metrics from cellranger across Illumina samples
ThreadText: # Aggregate sequencing/mapping/etc. metrics from cellranger across Illumina samples
  
  (Asked by: username_0 on 2018-03-01)
  
  I have a number of single-cell projects processed with [cellranger from 10x Genomics](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The pipeline produces a number of handy metrics that are summarized for each Illumina sample in [web page](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/summary). These include things like the estimated number of cells, the fraction of reads in cells, and mapping rates. What I would like is to aggregate this information from multiple Illumina samples into a single file. [MultiQC](http://multiqc.info/) is the obvious choice for such a task, but it appears that no one has written a module to process cellranger data for it. Are there any other prepackaged ways to perform this aggregation?
  
  If there's no convenient tool for this I'll just write a MultiQC module, but I'd obviously like to avoid the extra effort unless it's really needed.
  
  **Tags:** scrnaseq, cellranger
  
  > **Comments:**
  > **username_1**: Single-cell RNA-seq analysis is still developing (not crystallized yet), so I think what you want is not there yet. If you think it may be handy for your analysis, many more may follow, so making a tool for this might be fruitful (if you make it available for others).  
  > **username_2**: We’ve written a MultiQC module for Supernova, but not Long ranger or Cell Ranger (yet). I agree that one would be useful, and probably quite quick to write if there’s also a JSON summary file output for that tool too. We’ve been talking about this recently. Did you ever get anywhere with writing a new module?  
  > **username_3**: any new about that? The cellranger is now version 5 and produce still data that would be great to compile in a single report.  
  > **username_4**: Things move fast.  Cellranger now has a version 6.0  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_5 on 2021-03-21. Score: 1
  
  I wrote a simple script to do it. Not sure whether that's what you want.
  
  ```
  #!/bin/bash
  #CellrangerSummary.sh Sample1 Sample2
  csvtool transpose $1/outs/*summary.csv | csvcut -c 1 > summary.csv
  for sample in "$@"
      do
          csvtool transpose $sample/outs/*summary.csv > tempfilesforcsvtool.$sample
          csvjoin -c 1 summary.csv tempfilesforcsvtool.$sample > temp2
      mv temp2 summary.csv
  rm tempfilesforcsvtool.$sample
      done
  
  csvformat -T summary.csv > summary.tsv
  rm summary.csv
  ```
  
  ```
  
  
  ---
  
  