These are the required command line arguments:

Optional command line parameters are listed below (also available through cellranger-arc reanalyze --help):

After determining input arguments and options, run cellranger-arc reanalyze. This example reanalyzes the results of an aggregation named AGG123 in order to filter out doublet barcodes:

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$ cd /home/jdoe/runs
$ ls -1 AGG123/outs/*.gz # verify the input file exists
AGG123/outs/fragments.tsv.gz
$ cellranger-arc reanalyze  --id=AGG123_reanalysis \
                            --barcodes=no_doublets.csv \
                            --matrix=/home/jdoe/runs/AGG123/outs/raw_feature_bc_matrix.h5 \
                            --reference=/home/jdoe/refs/hg19 \
                            --atac-fragments=/home/jdoe/runs/AGG123/outs/atac_fragments.tsv.gz

The pipeline will begin to run, creating a new folder named with the reanalysis ID specified with the --id argument (e.g. /home/jdoe/runs/AGG123_reanalysis) for its output. If this output folder already exists, cellranger-arc will assume it is an existing pipestance and attempt to resume running it.

A successful run should conclude with a message similar to this:

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2021-04-26 03:30:46 [runtime] (update)          ID.AGG123_reanalysis.SC_ATAC_GEX_REANALYZER_CS.ATAC_GEX_CLOUPE_PREPROCESS.fork0 join_running
2021-04-26 03:36:05 [runtime] (join_complete)   ID.AGG123_reanalysis.SC_ATAC_GEX_REANALYZER_CS.ATAC_GEX_CLOUPE_PREPROCESS

Outputs:
- Secondary analysis outputs:
    clustering:
      atac: {
        ...
      }
      gex:  {
        ...
      }
    dimensionality_reduction:
      atac: {
        ...
      }
      gex:  {
        ...
      }
    feature_linkage:
      ...
    tf_analysis:
      ...
- Filtered feature barcode matrix HDF5:          /home/jdoe/runs/AGG123_reanalysis/outs/filtered_feature_bc_matrix.h5
- Loupe browser visualization file:              /home/jdoe/runs/AGG123_reanalysis/outs/cloupe.cloupe
- ATAC peak annotations based on proximal genes: /home/jdoe/runs/AGG123_reanalysis/outs/atac_peak_annotation.tsv
- Secondary analysis summary:                    /home/jdoe/runs/AGG123_reanalysis/outs/summary.json

Pipestance completed successfully!

Refer to the Multiome ATAC + Gene Expression Analysis page for an explanation of the output.

The CSV file passed to --params should have one row for every parameter that you want to customize. There is no header row. If a parameter is not specified in your CSV, its default value will be used.

Here are detailed descriptions of each parameter. For parameters that subset the data, a default value of null indicates that no subsetting happens by default.