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# Summary Metrics

The cellranger-atac count pipeline outputs summary.csv which contains a number of key metrics in text, csv format. Below are the definitions of the reported metrics. When the metric is species specific, a value is reported for each species in multi-species experiments. When a metric is not computed by the pipeline, likely because of insufficient information or divison by zero, it is not reported in the summary.csv.

MetricDescriptionIs Species Specific
Sample ID Value of --id passed to the pipeline. FALSE
Genome Reference genome used for the analysis. FALSE
Estimated number of cells The total number of barcodes identified as cells. TRUE
Confidently mapped read pairs Fraction of sequenced read pairs with mapping quality > 30 FALSE
Estimated bulk library complexity Estimated complexity of the library given the observed unique read pairs when sequenced to current depth. FALSE
Fraction of genome in peaks Fraction of bases in primary contigs that are defined as peaks. FALSE
Fraction of high-quality fragments in cells Fraction of high-quality fragments with a valid barcode that are associated with cell-containing partitions. High-quality fragments are defined as read pairs with a valid barcode that map to the nuclear genome with mapping quality > 30, are not chimeric and not duplicate. FALSE
Fraction of high-quality fragments overlapping TSS Fraction of high-quality fragments in cell barcodes that overlap transcription start sites (TSS). TRUE
Fraction of high-quality fragments overlapping peaks Fraction of high-quality fragments in cell barcodes that overlap called peaks. TRUE
Fraction of transposition events in peaks in cells Fraction of transposition events that are associated with cell-containing partitions and fall within peaks. Transposition events are located at both ends of all high-quality fragments. This metric measures the percentage of such events that overlap with peaks. FALSE
Fragments flanking a single nucleosome Fraction of high-quality fragments between 147 and 294 basepairs. FALSE
Fragments in nucleosome-free regions Fraction of high-quality fragments smaller than 147 basepairs. FALSE
Inferred multiplet rate The estimated fraction of cell barcodes containing more than one cell. FALSE
Mean raw read pairs per cell Total number of read pairs divided by the number of cell barcodes TRUE
Median barcode purity The median, across all cell barcodes, of the fraction of fragments in the barcode that align uniquely to the species assigned to the barcode. TRUE
Median high-quality fragments per cell The median number of high-quality fragments per cell barcode TRUE
Non-nuclear read pairs Fraction of sequenced read pairs that have a valid barcode and map to non-nuclear genome contigs, including mitochondria,with mapping quality > 30. FALSE
Number of peaks Total number of peaks on primary contigs either detected by the pipeline or input by the user. FALSE
Observed multiplet rate The observed fraction of cell barcodes that appear to have cells from both species present. FALSE
Percent duplicates Fraction of high-quality read pairs that are deemed to be PCR duplicates. A high-quality read-pair is one with mapping quality > 30, that is not chimeric and maps to nuclear contigs. This metric is a measure of sequencing saturation and is a function of library complexity and sequencing depth. More specifically, this is the fraction of high-quality fragments with a valid barcode that align to the same genomic position as another read pair in the library. FALSE
Post-Normalization median unique fragments per cell in library The median unique fragments per cell barcode in the library after normalization TRUE
Post-Normalization total mapped read pairs The total fragments (mapped read pairs) after normalization FALSE
Post-Normalization total mapped read pairs in library The total fragments (mapped read pairs) in the library after normalization TRUE
Post-Normalization unique fragments in library The unique fragments (mapped read pairs) in the library after normalization TRUE
Pre-Normalization median unique fragments per cell in library The median unique fragments per cell barcode in the library before normalization TRUE
Pre-Normalization total mapped read pairs The total fragments (mapped read pairs) before normalization FALSE
Pre-Normalization total mapped read pairs in library The total fragments (mapped read pairs) in the library before normalization TRUE
Pre-Normalization unique fragments in library The unique fragments (mapped read pairs) in the library before normalization TRUE
Q30 bases in barcode Fraction of barcode read (i5 index read) bases with Q-score >= 30. FALSE
Q30 bases in read 1 Fraction of read 1 bases with Q-score >= 30. FALSE
Q30 bases in read 2 Fraction of read 2 bases with Q-score >= 30. FALSE
Q30 bases in sample index i1 Fraction of sample index read (i7 index read) bases with Q-score >= 30. FALSE
Sequenced read pairs Total number of sequenced read pairs assigned to the sample. FALSE
Sequencing saturation Estimated sequencing saturation of high-quality fragment pool. Computed as the ratio of observed unique read pairs to estimated library complexity. FALSE
TSS enrichment score Maximum value of the transcription-start-site (TSS) profile.The TSS profile is the summed accessibility signal (defined as number of cut sites per base) in a window of 2,000 bases around all the annotated TSSs, normalized by the minimum signal in the window. FALSE
Unmapped read pairs Fraction of sequenced read pairs that have a valid barcode but could not be mapped to the genome FALSE
Valid barcodes Fraction of read pairs with barcodes that match the whitelist after error correction. FALSE

## Cell Ranger ATAC Aggregator Metrics Definitions

The cellranger-atac aggr pipeline outputs summary.json which contains metrics relating to the aggregated datasets. Note: brackets denote a variable that depends on the pipeline input, e.g. post_norm_median_frags_per_cell_Library_{library} means that if your aggregation contains two libraries with IDs sample123 and sample456, there will be two output metrics: post_norm_median_frags_per_cell_Library_sample123 and post_norm_median_frags_per_cell_Library_sample456.

MetricDescriptionIs Species Specific
annotated_cellsEstimated number of cells.True
cellranger-atac_versionSoftware version used to run the pipeline.False
frac_cut_fragments_in_peaksFraction of transposition events in peaks.False
frac_fragments_overlapping_peaksFraction of fragments overlapping called peaks.True
frac_fragments_overlapping_targetsFraction of fragments overlapping any targeted region.True
median_fragments_per_cellMedian fragments per cell barcode.True
post_norm_median_frags_per_cell_Library_{}Post-Normalization median unique fragments per cell in libraryFalse
pre_norm_median_frags_per_cell_Library_{}Pre-Normalization median unique fragments per cell in libraryFalse
total_post_normalization_Library_{}Post-Normalization total mapped read pairs in libraryFalse
total_pre_normalization_Library_{}Pre-Normalization total mapped read pairs in libraryFalse
unique_post_normalization_Library_{}Post-Normalization unique fragments in libraryFalse
unique_pre_normalization_Library_{}Pre-Normalization unique fragments in libraryFalse
total_post_normalizationPost-Normalization total mapped read pairsFalse
total_pre_normalizationPre-Normalization total mapped read pairsFalse