10x Genomics Support/Cell Ranger 7.2/Analysis/

Metrics Outputs from the Cell Ranger aggr Pipeline

The cellranger aggr pipeline outputs summary.json which contains metrics relating to the aggregated datasets. Note: square brackets denote a variable that depends on the pipeline input, e.g. [library_id]_frac_reads_kept means that if your aggregation contains two libraries with IDs sample123 and sample456, there will be two output metrics sample123_frac_reads_kept and sample456_frac_reads_kept.

MetricDescription
filtered_bcs_transcriptome_unionThe estimated number of barcodes associated with cell-containing partitions, summed across all input libraries.
total_readsTotal number of sequenced reads, summed across all input libraries.
multi_transcriptome_total_raw_reads_per_filtered_bctotal_reads divided by filtered_bcs_transcriptome_union.
[library_id]_pre_normalization_raw_reads_per_filtered_bcThe mean total reads per cell prior to depth normalization, for the library denoted by library_id.
[library_id]_pre_normalization_cmb_reads_per_filtered_bcThe mean confidently mapped and barcoded (CMB) reads per cell prior to depth normalization, for the library denoted by library_id.
[library_id]_frac_reads_keptThe fraction of reads that were retained after depth normalization for the library denoted by library_id.
lowest_frac_reads_keptThe lowest fraction of reads retained, corresponding to the library which lost the most reads during normalization. A low value may indicate a large disparity in the initial depth of the input libraries.