text: user77: I have a number of single-cell projects processed with cellranger from 10x Genomics. The pipeline produces a number of handy metrics that are summarized for each Illumina sample in web page. 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 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.
  
  user1852: 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
  ```
  
  
original_text: 77: <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>
   1852: <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>
  