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Metrics Outputs from the Cell Ranger aggr Pipeline

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.