Key Influencers Analysis

Target Metric (What to Explain) Select a metric to analyze... Antibody: Antibody Reads Usable per Cell Antibody: Antibody Reads in Cells Antibody: Fraction Antibody Reads Antibody: Fraction Antibody Reads Usable Antibody: Fraction Antibody Reads in Aggregate Barcodes Antibody: Fraction Reads in Barcodes with High UMI Counts Antibody: Fraction Unrecognized Antibody Antibody: Mean Reads per Cell Antibody: Median UMIs per Cell (summed over all recognized antibody barcodes) Antibody: Number of Reads Antibody: Q30 Bases in Antibody Read Antibody: Q30 Bases in Antibody Read 2 Antibody: Q30 Bases in Barcode Antibody: Q30 Bases in UMI Antibody: Sequencing Saturation Antibody: Valid Barcodes Cells - Antibody Capture - Antibody reads in cells Cells - Antibody Capture - Cells Cells - Antibody Capture - Fraction antibody reads Cells - Antibody Capture - Fraction antibody reads in aggregate barcodes Cells - Antibody Capture - Mean antibody reads usable per cell Cells - Antibody Capture - Median UMI counts per cell Cells - Antibody Capture - Number of reads from cells associated with this sample Cells - CRISPR Guide Capture - Cells Cells - CRISPR Guide Capture - Cells with one or more protospacers detected Cells - CRISPR Guide Capture - Cells with two or more protospacers detected Cells - CRISPR Guide Capture - Fraction guide reads Cells - CRISPR Guide Capture - Fraction protospacer not recognized Cells - CRISPR Guide Capture - Fraction reads with putative protospacer sequence Cells - CRISPR Guide Capture - Guide reads in cells Cells - CRISPR Guide Capture - Mean guide reads usable per cell Cells - CRISPR Guide Capture - Median UMI counts per cell Cells - CRISPR Guide Capture - Number of reads from cells associated with this sample Cells - Gene Expression - Cells Cells - Gene Expression - Confidently mapped reads in cells Cells - Gene Expression - Mean reads per cell Cells - Gene Expression - Median UMI counts per cell Cells - Gene Expression - Median genes per cell Cells - Gene Expression - Total genes detected Cells - VDJ B - Cells with productive IGH contig Cells - VDJ B - Cells with productive IGK contig Cells - VDJ B - Cells with productive IGL contig Cells - VDJ B - Cells with productive V-J spanning (IGK, IGH) pair Cells - VDJ B - Cells with productive V-J spanning (IGL, IGH) pair Cells - VDJ B - Cells with productive V-J spanning pair Cells - VDJ B - Estimated number of cells Cells - VDJ B - Median IGH UMIs per Cell Cells - VDJ B - Median IGK UMIs per Cell Cells - VDJ B - Median IGL UMIs per Cell Cells - VDJ B - Number of cells with productive V-J spanning pair Cells - VDJ B - Paired clonotype diversity Cells - VDJ T - Cells with productive TRA contig Cells - VDJ T - Cells with productive TRB contig Cells - VDJ T - Cells with productive V-J spanning (TRA, TRB) pair Cells - VDJ T - Cells with productive V-J spanning pair Cells - VDJ T - Estimated number of cells Cells - VDJ T - Fraction reads in cells Cells - VDJ T - Median TRA UMIs per Cell Cells - VDJ T - Median TRB UMIs per Cell Cells - VDJ T - Number of cells with productive V-J spanning pair Cells - VDJ T - Paired clonotype diversity Cells - VDJ T - VDJ cells Cells With CDR3-annotated IGH Contig Cells With CDR3-annotated IGK Contig Cells With CDR3-annotated IGL Contig Cells With CDR3-annotated TRA Contig Cells With CDR3-annotated TRB Contig Cells With IGH Contig Cells With IGK Contig Cells With IGL Contig Cells With Productive IGH Contig Cells With Productive IGK Contig Cells With Productive IGL Contig Cells With Productive TRA Contig Cells With Productive TRB Contig Cells With Productive V-J Spanning (IGK, IGH) Pair Cells With Productive V-J Spanning (IGL, IGH) Pair Cells With Productive V-J Spanning (TRA, TRB) Pair Cells With Productive V-J Spanning Pair Cells With TRA Contig Cells With TRB Contig Cells With V-J Spanning IGH Contig Cells With V-J Spanning IGK Contig Cells With V-J Spanning IGL Contig Cells With V-J Spanning TRA Contig Cells With V-J Spanning TRB Contig Confidently mapped read pairs Estimated Number of Cells Estimated bulk library complexity Estimated number of cells Fraction Reads in Cells Fraction of all fragments in cells Fraction of all fragments that pass all filters and overlap called peaks Fraction of genome in peaks Fraction of high-quality fragments in cells Fraction of high-quality fragments overlapping TSS Fraction of high-quality fragments overlapping peaks Fraction of transposition events in peaks in cells Fragments flanking a single nucleosome Fragments in nucleosome-free regions Genome Group Name Grouped By Library - Antibody Capture - Antibody reads in cells Library - Antibody Capture - Estimated number of cells Library - Antibody Capture - Fraction antibody reads Library - Antibody Capture - Fraction antibody reads in aggregate barcodes Library - Antibody Capture - Fraction antibody reads usable Library - Antibody Capture - Mean reads per cell Library - Antibody Capture - Number of reads Library - Antibody Capture - Number of reads in the library Library - Antibody Capture - Number of short reads skipped Library - Antibody Capture - Q30 RNA read Library - Antibody Capture - Q30 RNA read 2 Library - Antibody Capture - Q30 UMI Library - Antibody Capture - Q30 barcodes Library - Antibody Capture - Sequencing saturation Library - Antibody Capture - Valid UMIs Library - Antibody Capture - Valid barcodes Library - CRISPR Guide Capture - Estimated number of cells Library - CRISPR Guide Capture - Fraction guide reads Library - CRISPR Guide Capture - Fraction guide reads usable Library - CRISPR Guide Capture - Fraction protospacer not recognized Library - CRISPR Guide Capture - Fraction reads with putative protospacer sequence Library - CRISPR Guide Capture - Guide reads in cells Library - CRISPR Guide Capture - Mean reads per cell Library - CRISPR Guide Capture - Number of reads Library - CRISPR Guide Capture - Number of short reads skipped Library - CRISPR Guide Capture - Q30 RNA read Library - CRISPR Guide Capture - Q30 UMI Library - CRISPR Guide Capture - Q30 barcodes Library - CRISPR Guide Capture - Sequencing saturation Library - CRISPR Guide Capture - Valid UMIs Library - CRISPR Guide Capture - Valid barcodes Library - Gene Expression - Cells Library - Gene Expression - Confidently mapped antisense Library - Gene Expression - Confidently mapped reads in cells Library - Gene Expression - Confidently mapped to exonic regions Library - Gene Expression - Confidently mapped to genome Library - Gene Expression - Confidently mapped to intergenic regions Library - Gene Expression - Confidently mapped to intronic regions Library - Gene Expression - Confidently mapped to transcriptome Library - Gene Expression - Estimated number of cells Library - Gene Expression - Mapped to genome Library - Gene Expression - Mean reads per cell Library - Gene Expression - Number of reads Library - Gene Expression - Number of reads in the library Library - Gene Expression - Number of short reads skipped Library - Gene Expression - Q30 RNA read Library - Gene Expression - Q30 RNA read 2 Library - Gene Expression - Q30 UMI Library - Gene Expression - Q30 barcodes Library - Gene Expression - Sequencing saturation Library - Gene Expression - Valid UMIs Library - Gene Expression - Valid barcodes Library - VDJ B - Estimated number of cells Library - VDJ B - Fraction reads in cells Library - VDJ B - Mean reads per cell Library - VDJ B - Mean used reads per cell Library - VDJ B - Number of reads Library - VDJ B - Number of short reads skipped Library - VDJ B - Q30 RNA read Library - VDJ B - Q30 RNA read 2 Library - VDJ B - Q30 UMI Library - VDJ B - Q30 barcodes Library - VDJ B - Reads mapped to IGH Library - VDJ B - Reads mapped to IGK Library - VDJ B - Reads mapped to IGL Library - VDJ B - Reads mapped to any V(D)J gene Library - VDJ B - Valid barcodes Library - VDJ T - Cells with productive TRA contig Library - VDJ T - Cells with productive TRB contig Library - VDJ T - Cells with productive V-J spanning (TRA, TRB) pair Library - VDJ T - Cells with productive V-J spanning pair Library - VDJ T - Estimated number of cells Library - VDJ T - Fraction reads in cells Library - VDJ T - Mean reads per cell Library - VDJ T - Mean used reads per cell Library - VDJ T - Number of reads Library - VDJ T - Number of short reads skipped Library - VDJ T - Q30 RNA read Library - VDJ T - Q30 RNA read 2 Library - VDJ T - Q30 UMI Library - VDJ T - Q30 barcodes Library - VDJ T - Reads mapped to TRA Library - VDJ T - Reads mapped to TRB Library - VDJ T - Reads mapped to any V(D)J gene Library - VDJ T - VDJ Cells Library - VDJ T - Valid barcodes Library Type Library or Sample Mean Read Pairs per Cell Mean Reads per Cell Mean Used Read Pairs per Cell Mean raw read pairs per cell Median Genes per Cell Median IGH UMIs per Cell Median IGK UMIs per Cell Median IGL UMIs per Cell Median TRA UMIs per Cell Median TRB UMIs per Cell Median UMI Counts per Cell Median high-quality fragments per cell Metric Name Metric Value Non-nuclear read pairs Number of Cells With Productive V-J Spanning Pair Number of Read Pairs Number of Reads Number of peaks Paired Clonotype Diversity Percent duplicates Pipeline version Q30 Bases in Barcode Q30 Bases in RNA Read Q30 Bases in RNA Read 1 Q30 Bases in RNA Read 2 Q30 Bases in Sample Index Q30 Bases in UMI Q30 bases in barcode Q30 bases in read 1 Q30 bases in read 2 Q30 bases in sample index i1 Reads Mapped Antisense to Gene Reads Mapped Confidently to Exonic Regions Reads Mapped Confidently to Genome Reads Mapped Confidently to Intergenic Regions Reads Mapped Confidently to Intronic Regions Reads Mapped Confidently to Transcriptome Reads Mapped to Any V(D)J Gene Reads Mapped to Genome Reads Mapped to IGH Reads Mapped to IGK Reads Mapped to IGL Reads Mapped to TRA Reads Mapped to TRB Sample ID Sequenced read pairs Sequencing Saturation Sequencing saturation TSS enrichment score Total Genes Detected Unmapped read pairs Valid Barcodes Valid barcodes annotated_cells bc_q30_bases_fract cellranger-atac_version cells_detected frac_cut_fragments_in_peaks frac_fragments_nfr frac_fragments_nfr_or_nuc frac_fragments_nuc frac_fragments_overlapping_peaks frac_fragments_overlapping_targets frac_mapped_confidently frac_waste_chimeric frac_waste_duplicate frac_waste_lowmapq frac_waste_mitochondrial frac_waste_no_barcode frac_waste_non_cell_barcode frac_waste_overall_nondup frac_waste_total frac_waste_unmapped median_fragments_per_cell median_per_cell_total_library_complexity num_fragments r1_q30_bases_fract r2_q30_bases_fract si_q30_bases_fract total_usable_fragments tss_enrichment_score

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