<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>

CC BY-SA 4.0
2021-03-21T19:41:00.850Z
2021-03-22T22:53:48.450Z
2021-03-22T22:53:48.450Z
Code42
<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>

CC BY-SA 3.0
2018-03-01T20:57:51.423Z
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).
benn
CC BY-SA 3.0
2018-03-11T15:57:38.897Z
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?
ewels
CC BY-SA 4.0
2021-03-16T09:59:08.877Z
any new about that? The cellranger is now version 5 and produce still data that would be great to compile in a single report.
Gildas
CC BY-SA 4.0
2021-03-16T20:19:02.033Z
Things move fast.  Cellranger now has a version 6.0
swbarnes2
<scrnaseq><cellranger>
Aggregate sequencing/mapping/etc. metrics from cellranger across Illumina samples
# 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
```


---

