Aggregates Table

Field	Used for cellranger count	Used for cellranger aggr	Used for non-10X Genomics	Required
sample	optional	yes	optional	yes, cellranger aggr
replicate	optional	yes	optional	yes, cellranger aggr
bc_suffix	optional	yes	optional	yes, cellranger aggr
library_id	optional	yes	optional	yes, cellranger aggr
metadata1	optional	optional	optional	optional

Note

• The aggregates table is optional and used to map library barcode labels to library IDs in aggregated input files. The aggregated input contains multiple biological replicates, which can be generated using cellranger-arc aggr (Multiome), cellranger-atac aggr (ATAC), or cellranger aggr (RNA).

• When creating loading matrices, multiome-wf will map values in library_id to the barcode suffix. If using 10X Genomics platforms, cellranger aggr appends the row number of the aggregates.csv to all barcodes for that rows sample_id.

• For details about 10X Genomic’s aggregates tables, see:

  • 10X Genomics Multiome Aggregation Page

  • 10X Genomics Gene Expression Aggregation Page

  • 10X Genomics ATAC Aggregation Page

Field descriptions

sample

string. Defines labels for each sample. Values in sample column must be unique, unless analyzing technical replicates. If specifying technical replicates, sample label must be the same for all rows containing technical replicates.

replicate

string. Optional. Defines labels for each technical replicate of a sample. Values in replicate column must be unique per sample. If not specified technical replicates, leave empty. If specified technical replicates: sample must be the same for all rows containing technical replicates.

Note

Refer to the Replicates section for the definition of biological and technical replicates.

bc_suffix

string. Optional. Defines a unique library label to all barcodes for each sample. If sample is output of cellranger aggr Values in bc_suffix column must be the row number (1 based) corresponding the sample_id value from cellranger aggr’s aggregation CSV.

If sample is output of non-10X Genomics platform Values in must be a unique library identifier appended to the barcode. Barcode and library suffix must be separated by a dash (-) in the following pattern: [barcode]-[bc_suffix].

library_id

string. Optional. Defines labels associated with library barcode suffix for each sample. Values in library_id column must be unique per sample. If sample is output of cellranger aggr Values in library_id column must be the ‘sample_id’ value from cellranger aggr’s aggregation CSV.

If sample is output of non-10X Genomics platform Values in must correspond to the unique library suffix specified in bc_suffix column.

metadata*

string. Optional. Define columns for metadata labels. Colums beginning with metadata are placeholders for user specified metadata. They can be re-renamed to any string, deleted, or additional metadata columns can be added.

Note

• In aggregates.tsv, the following column names are considered immutable: “sample”, “replicate”, “bc_suffix”, “library_id”.

• Any additional columns present in aggregates.tsv will be considered metadata columns. Metadata columns can have any unique label, not just the “meta*” used in the example samples table.

Example

Multiome

a basic example of an aggregation CSV passed to the --csv parameter of cellranger-arc aggr (upper table) and an aggregates.tsv file configured for multiome-wf pipeline (lower table):

sample	replicate	library_id	library_id	metadata1
rep1_wt		1	1	wt
rep1_homo		2	2	ko

library_id	atac_fragments	per_barcode_metrics	gex_molecule_info
rep1_wt	rep1_wt/outs/atac_fragments.tsv.gz	rep1_wt/outs/per_barcode_metrics.csv	rep1_wt/out/gex_molecule_info.h5
rep1_homo	rep1_homo/outs/atac_fragments.tsv.gz	rep1_homo/outs/per_barcode_metrics.csv	rep1_homo/out/gex_molecule_info.h5

RNA-seq

a basic example of an aggregation CSV passed to the --csv parameter of cellranger aggr (upper table) and an aggregates.tsv file configured for multiome-wf pipeline (lower table):

sample_id	molecule_h5
CTX	CTX/outs/molecule_info.h5
MGE	MGE/outs/molecule_info.h5

sample	replicate	library_id	bc_suffix	meta_tissue
CTX		1	1	CTX
MGE		2	2	MGE

ATAC-seq

a basic example of an aggregation CSV passed to the --csv parameter of cellranger-atac aggr (upper table) and an aggregates.tsv file configured for multiome-wf pipeline (lower table):

library_id	fragments	cells
CTX	CTX_rerun/outs/fragments.tsv.gz	CTX_rerun/outs/singlecell.csv
MGE	MGE_rerun/outs/fragments.tsv.gz	MGE_rerun/outs/singlecell.csv

sample	replicate	library_id	bc_suffix	meta_tissue
CTX		1	1	CTX
MGE		2	2	MGE

See Overview of workflows for more detailed examples of config files.