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.

  • $\begingroup$ 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). $\endgroup$
    – benn
    Commented Mar 1, 2018 at 20:57
  • $\begingroup$ 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? $\endgroup$
    – ewels
    Commented Mar 11, 2018 at 15:57
  • $\begingroup$ any new about that? The cellranger is now version 5 and produce still data that would be great to compile in a single report. $\endgroup$
    – Gildas
    Commented Mar 16, 2021 at 9:59
  • $\begingroup$ Things move fast. Cellranger now has a version 6.0 $\endgroup$
    – swbarnes2
    Commented Mar 16, 2021 at 20:19

1 Answer 1


I wrote a simple script to do it. Not sure whether that's what you want.

#CellrangerSummary.sh Sample1 Sample2
csvtool transpose $1/outs/*summary.csv | csvcut -c 1 > summary.csv
for sample in "$@"
        csvtool transpose $sample/outs/*summary.csv > tempfilesforcsvtool.$sample
        csvjoin -c 1 summary.csv tempfilesforcsvtool.$sample > temp2
    mv temp2 summary.csv
rm tempfilesforcsvtool.$sample

csvformat -T summary.csv > summary.tsv
rm summary.csv

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