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10x Genomics
Chromium Single Cell ATAC

Aggregating Multiple GEM Wells with cellranger-atac aggr

Table of Contents

What is aggr?

Many experiments involve generating data for multiple samples that are processed through different Gel Bead-in Emulsion (GEM) wells on Chromium instruments. Depending on the experimental design, these could be replicates from the same set of cells, cells from different tissues or time points from the same individual, or cells from different individuals. The cellranger-atac aggr pipeline can be used to aggregate these into a single peak-barcode matrix.

When conducting large studies involving multiple GEM wells, run cellranger-atac count on FASTQ data from each of the GEM wells individually, then pool the results using cellranger-atac aggr, as described here.

The cellranger-atac aggr command inputs a CSV file specifying a list of cellranger-atac count output files (specifically the fragments.tsv.gz, and singlecell.csv from each run), and produces a single peak-barcode matrix containing all the data.

When combining multiple GEM wells, the barcode sequences for each channel are distinguished by a GEM well suffix appended to the barcode sequence (see GEM wells).

By default, the reads from each GEM well are subsampled such that all GEM wells have the same effective sequencing depth, measured in terms of the median number of unique fragments per cell. However, it is possible to turn off this normalization altogether (see Depth Normalization).

Understanding GEM wells

Each GEM well is a physically distinct set of GEM partitions corresponding to a single Chromium chip channel, but draws barcode sequences randomly from the pool of valid barcodes, known as the barcode whitelist. To keep the barcodes unique when aggregating multiple libraries, Cell Ranger ATAC appends a small integer identifying the GEM well to the barcode nucleotide sequence, and uses that nucleotide sequence plus ID as the unique identifier in the feature-barcode matrix. For example, AGACCATTGAGACTTA-1 and AGACCATTGAGACTTA-2 are distinct cell barcodes from different GEM wells, despite having the same barcode nucleotide sequence.

This number, which indicates which GEM well the barcode sequence came from, is called the GEM well suffix. The numbering of the GEM wells will reflect the order that the GEM wells were provided in the Aggregation CSV.

Requirements

Prior to aggregating data, first run a single instance of cellranger-atac count on each individual GEM well prepared using the Chromium platform, as described in single GEM well analysis.

For example, suppose you ran three count pipelines as follows:

$ cd /opt/runs
$ cellranger-atac count --id=LV123 ...
... wait for pipeline to finish ...
$ cellranger-atac count --id=LV456 ...
... wait for pipeline to finish ...
$ cellranger-atac count --id=LV789 ...
... wait for pipeline to finish ...

You can aggregate these three runs to get an aggregated matrix and analysis. In order to do so, you need to create an Aggregation CSV as detailed in the next section.

Create aggregation CSV

Create a CSV file with a header line containing the following columns:

You can either make the CSV file in a text editor, or create it in Excel and export to CSV. Continuing the example from the previous section, your Excel spreadsheet should look like this:

ABC
1library_idfragmentscells
2LV123/opt/runs/LV123/outs/fragments.tsv.gz/opt/runs/LV123/outs/singlecell.csv
3LV456/opt/runs/LV456/outs/fragments.tsv.gz/opt/runs/LV456/outs/singlecell.csv
4LV789/opt/runs/LV789/outs/fragments.tsv.gz/opt/runs/LV789/outs/singlecell.csv

When you save it as a CSV, the result looks like this:

library_id,fragments,cells
LV123,/opt/runs/LV123/outs/fragments.tsv.gz,/opt/runs/LV123/outs/singlecell.csv
LB456,/opt/runs/LB456/outs/fragments.tsv.gz,/opt/runs/LB456/outs/singlecell.csv
LP789,/opt/runs/LP789/outs/fragments.tsv.gz,/opt/runs/LP789/outs/singlecell.csv

Running aggr on the command line

These are the required command line arguments (also available through cellranger-atac aggr --help):

ArgumentDescription
--id=IDA unique run id and output folder name [a-zA-Z0-9_-]+ of maximum length 64 characters.
--csv=CSVPath to CSV file enumerating cellranger-atac count outputs (see Setting up a CSV).
--reference=PATHPath to folder containing a Cell Ranger ATAC or Cell Ranger ARC reference.

Additional optional parameters are available:

OptionDescription
--description=TEXTSample description to embed in output files [default: ]
--peaks=BEDOverride peak caller: specify peaks to use in downstream analyses from supplied 3-column BED file. The supplied peaks file must be sorted by position and not contain overlapping peaks; comment lines beginning with # are allowed
--normalize=MODELibrary depth normalization mode [default: depth] [possible values: depth, none]
--dim-reduce=STRDimensionality reduction mode for clustering. Note: plsa has been temporarily restricted to run in single-threaded mode due to technical considerations. This could lead to a longer wall time for execution as compared to v1.2. Multi-threading will be restored in a subsequent release [default: lsa] [possible values: lsa, pca, plsa]
--jobmode=MODEJob manager to use. Valid options: local (default), sge, lsf, slurm or path to a .template file. Search for help on "Cluster Mode" at support.10xgenomics.com for more details on configuring the pipeline to use a compute cluster [default: local]
--localcores=NUMSet max cores the pipeline may request at one time. Only applies to local jobs
--localmem=NUMSet max memory (GB) the pipeline may request at one time. Only applies to local jobs
--localvmem=NUMSet max virtual address space in GB for the pipeline. Only applies to local jobs
--mempercore=NUMReserve enough threads for each job to ensure enough memory will be available, assuming each core on your cluster has at least this much memory available. Only applies to cluster jobmodes
--maxjobsSet max jobs submitted to cluster at one time. Only applies to cluster jobmodes
--jobintervalSet delay between submitting jobs to cluster, in ms. Only applies to cluster jobmodes
--overrides=PATHThe path to a JSON file that specifies stage-level overrides for cores and memory. Finer-grained than --localcores, --mempercore and --localmem. Consult https://support.10xgenomics.com/ for an example override file
--uiport=PORTServe web UI at http://localhost:PORT

After specifying input arguments and options, run cellranger-atac aggr:

$ cd /home/jdoe/runs
$ cellranger-atac aggr  --id=AGG123 \
                        --csv=AGG123_libraries.csv \
                        --normalize=depth \
                        --reference=/home/jdoe/refs/hg19

The pipeline will begin to run, creating a new folder named with the aggregation ID specified with the --id argument (e.g. /home/jdoe/runs/AGG123). If this output folder already exists, cellranger-atac will assume it is an existing pipestance and attempt to resume running it.

Pipeline outputs

The cellranger-atac aggr pipeline generates output files that contain all of the data from the individual input jobs, aggregated into single output files, for convenient multi-sample analysis. The GEM well suffix of each barcode is updated to prevent barcode collisions, as described below.

Each output file produced by cellranger-atac aggr follows the format described in the Understanding Output section, but includes the union of all the relevant barcodes from each input job.

A successful run will conclude with a message like this:

2021-04-24 14:06:25 [runtime] (update)          ID.AGG123.SC_ATAC_AGGREGATOR_CS.SC_ATAC_AGGREGATOR.ATAC_CLOUPE_PREPROCESS.fork0 join_running
2021-04-24 14:07:13 [runtime] (join_complete)   ID.AGG123.SC_ATAC_AGGREGATOR_CS.SC_ATAC_AGGREGATOR.ATAC_CLOUPE_PREPROCESS
 
Outputs:
- Barcoded and aligned fragment file:           /home/jdoe/runs/AGG123/outs/fragments.tsv.gz
- Fragment file index:                          /home/jdoe/runs/AGG123/outs/fragments.tsv.gz.tbi
- Per-barcode fragment counts & metrics:        /home/jdoe/runs/AGG123/outs/singlecell.csv
- Bed file of all called peak locations:        /home/jdoe/runs/AGG123/outs/peaks.bed
- Filtered peak barcode matrix in hdf5 format:  /home/jdoe/runs/AGG123/outs/filtered_peak_bc_matrix.h5
- Filtered peak barcode matrix in mex format:   /home/jdoe/runs/AGG123/outs/filtered_peak_bc_matrix
- Directory of analysis files:                  /home/jdoe/runs/AGG123/outs/analysis
- HTML file summarizing aggregation analysis :  /home/jdoe/runs/AGG123/outs/web_summary.html
- Filtered tf barcode matrix in hdf5 format:    /home/jdoe/runs/AGG123/outs/filtered_tf_bc_matrix.h5
- Filtered tf barcode matrix in mex format:     /home/jdoe/runs/AGG123/outs/filtered_tf_bc_matrix
- Loupe Browser input file:                /home/jdoe/runs/AGG123/outs/cloupe.cloupe
- csv summarizing important metrics and values: /home/jdoe/runs/AGG123/outs/summary.csv
- Summary of all data metrics:                  /home/jdoe/runs/AGG123/outs/summary.json
- Annotation of peaks with genes:               /home/jdoe/runs/AGG123/outs/peak_annotation.tsv
- Csv of aggregation of libraries:              /home/jdoe/runs/AGG123/outs/aggregation_csv.csv
 
Pipestance completed successfully!

Once cellranger-atac aggr has successfully completed, you can browse the resulting summary HTML file in any supported web browser, open the .cloupe file in Loupe Browser, or refer to the Understanding Output section to explore the data by hand. For machine-readable versions of the summary metrics, refer to the cellranger-atac aggr section of the Summary Metrics page.

Aggregating libraries with different chemistry versions

If you are aggregating libraries generated by different chemistry versions (v2 vs. v1.1) of the Single Cell ATAC reagents (not to be confused with the Cell Ranger ATAC pipeline version), you might observe systematic differences in chromatin accessibility profiles between libraries. The cellranger-atac aggr pipeline optionally incorporates batch effect correction (algorithm details) to overcome this. To enable this module, you should include the following column in your aggregation CSV file:

For example, if the LV123 sample in the previous example is a v1.1 chemistry library, and the LB456 and LP789 samples are v2 libraries, you would set up the aggregation CSV file like this:

library_id,fragments,cells,batch
LV123,/opt/runs/LV123/outs/fragments.tsv.gz,/opt/runs/LV123/outs/singlecell.csv,v1.1_lib
LV456,/opt/runs/LV456/outs/fragments.tsv.gz,/opt/runs/LV456/outs/singlecell.csv,v2_lib
LV789,/opt/runs/LV789/outs/fragments.tsv.gz,/opt/runs/LV789/outs/singlecell.csv,v2_lib

The v1.1_lib and v2_lib identifiers are merely example identifiers. Every sample from a given batch has to have the same batch identifier, but otherwise the identifier itself is arbitrary.

About chemistry batch correction

Depth normalization

When combining data from multiple GEM wells, the cellranger-atac aggr pipeline automatically equalizes the average read depth per cell between groups before merging. When libraries are sequenced to very different read depth per cell you may observe that cells cluster by library of origin rather than cell type. This is commonly referred to as a batch effect in the literature. A multitude of factors can cause batch effects in single cell data and sequencing depth is only one of them. The downsampling normalization in cellranger-atac aggr specifically addresses sequencing depth batch effects but not others. It is possible to turn off normalization or change the way normalization is done. The none option may be appropriate if you want to maximize sensitivity and plan to deal with depth normalization or more general batch correction in a downstream step.

There are two normalization modes: