Cell Ranger ATAC1.1, printed on 12/23/2024
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.
| Metric | Description | Is Species Specific |
|---|---|---|
median_fragments_per_cell | Median fragments per cell barcode. | True |
median_per_cell_total_library_complexity | Estimated median per cell library complexity. | False |
median_per_cell_unique_fragments_at_50000_RRPC | Median unique fragments per cell after downsampling to 50K raw reads per cell. | True |
median_per_cell_unique_fragments_at_30000_RRPC | Median unique fragments per cell after downsampling to 30K raw reads per cell. | True |
frac_cut_fragments_in_peaks | Fraction of transposition events in peaks. | False |
frac_fragments_nfr | Fragments in nucleosome-free regions. | False |
frac_fragments_nuc | Fragments flanking a single nucleosome. | False |
frac_fragments_nfr_or_nuc | Fragments in nucleosome-free or single-nucleosome regions. | False |
frac_fragments_overlapping_targets | Fraction of fragments overlapping any targeted region. | True |
frac_fragments_overlapping_peaks | Fraction of fragments overlapping called peaks. | True |
tss_enrichment_score | Enrichment score of transcription start sites. | False |
bc_q30_bases_fract | Q30 bases in Barcode. | False |
r1_q30_bases_fract | Q30 bases in Read 1. | False |
r2_q30_bases_fract | Q30 bases in Read 2. | False |
si_q30_bases_fract | Q30 bases in Sample Index. | False |
frac_waste_no_barcode | Fraction of read pairs with invalid barcodes. | False |
frac_waste_overall_nondup | Fraction of total read pairs that are non-duplicate and wasted read pairs. | False |
frac_waste_non_cell_barcode | Fraction of total read pairs in non-cell barcodes. | False |
frac_waste_chimeric | Fraction of total read pairs that are improper pairs or map to a supplementary contig and are in cell barcodes. | False |
frac_waste_mitochondrial | Fraction of total read pairs in mitochondria and in cell barcodes. | False |
frac_waste_unmapped | Fraction of total read pairs that are unmapped and in cell barcodes. | False |
frac_waste_lowmapq | Fraction of total read pairs that have low mapping quality and are in cell barcodes. | False |
frac_waste_duplicate | Percent duplicates. | False |
frac_waste_total | Fraction of total read pairs wasted (either have invalid barcodes or in non cell barcodes, or did not pass filters). | False |
total_usable_fragments | Total number of read pairs in cell barcodes passing all filters. | False |
frac_mapped_confidently | Fraction of total read pairs mapped confidently to genome (>30 mapq). | False |
num_fragments | Total number of read pairs. | False |
cellranger-atac_version | Software version used to run the pipeline. | False |
cells_detected | Number of barcodes identified as cells. | False |
annotated_cells | Estimated number of cells. | True |
observed_doublet_rate | Observed multiplet rate. | False |
inferred_doublet_rate | Inferred multiplet rate. | False |
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.
| Metric | Description | Is Species Specific |
|---|---|---|
annotated_cells | Estimated number of cells. | True |
cellranger-atac_version | Software version used to run the pipeline. | False |
frac_cut_fragments_in_peaks | Fraction of transposition events in peaks. | False |
frac_fragments_overlapping_peaks | Fraction of fragments overlapping called peaks. | True |
frac_fragments_overlapping_targets | Fraction of fragments overlapping any targeted region. | True |
median_fragments_per_cell | Median fragments per cell barcode. | True |
post_norm_median_frags_per_cell_Library_{} | Post-Normalization median unique fragments per cell in library | False |
pre_norm_median_frags_per_cell_Library_{} | Pre-Normalization median unique fragments per cell in library | False |
total_post_normalization_Library_{} | Post-Normalization total mapped read pairs in library | False |
total_pre_normalization_Library_{} | Pre-Normalization total mapped read pairs in library | False |
unique_post_normalization_Library_{} | Post-Normalization unique fragments in library | False |
unique_pre_normalization_Library_{} | Pre-Normalization unique fragments in library | False |
total_post_normalization | Post-Normalization total mapped read pairs | False |
total_pre_normalization | Pre-Normalization total mapped read pairs | False |