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10x Genomics
Chromium Single Cell Multiome ATAC + Gene Exp.

Per Barcode QC Metrics

The cellranger-arc count pipeline outputs per_barcode_metrics.csv, which contains metrics for every observed barcode. The columns contain the paired ATAC and Gene Expression barcode sequences, ATAC and Gene Expression QC metrics for that barcode, as well as whether this barcode was identified as a cell-associated partition by the pipeline.

Structure

The structure and contents of per_barcode_metrics.csv are shown below:

$ cd /home/jdoe/runs/sample345/outs
$ head -4 per_barcode_metrics.csv
barcode,gex_barcode,atac_barcode,is_cell,excluded_reason,gex_raw_reads,gex_mapped_reads,gex_conf_intergenic_reads,gex_conf_exonic_reads,gex_conf_intronic_reads,gex_conf_exonic_unique_reads,gex_conf_exonic_antisense_reads,gex_conf_exonic_dup_reads,gex_exonic_umis,gex_conf_intronic_unique_reads,gex_conf_intronic_antisense_reads,gex_conf_intronic_dup_reads,gex_intronic_umis,gex_conf_txomic_unique_reads,gex_umis_count,gex_genes_count,atac_raw_reads,atac_unmapped_reads,atac_lowmapq,atac_dup_reads,atac_chimeric_reads,atac_mitochondrial_reads,atac_fragments,atac_TSS_fragments,atac_peak_region_fragments,atac_peak_region_cutsites
AAACAGCCAAACAACA-1,AAACAGCCAAACAACA-1,ACAGCGGGTGTGTTAC-1,0,0,11,10,1,7,2,6,1,4,2,0,2,0,0,6,2,2,9,0,2,1,0,0,6,4,6,12
AAACAGCCAAACATAG-1,AAACAGCCAAACATAG-1,ACAGCGGGTTGTTCTT-1,0,2,7,7,0,6,1,6,0,5,1,0,1,0,0,6,1,1,3,0,2,0,0,0,1,0,0,0
AAACAGCCAAATATCC-1,AAACAGCCAAATATCC-1,ACAGCGGGTTGTGACT-1,1,0,58263,56138,2528,33577,17962,31480,1827,27942,3431,11276,6479,9899,1316,30809,4747,2272,16029,141,1332,6440,157,22,7937,4822,7074,13986

Column Definitions

MetricTypeDescription
barcodekeybarcode sequence associated with this data
gex_barcodekeyGene Expression library barcode sequence, identical to barcode
atac_barcodekeypaired ATAC library barcode sequence
is_cellcell callingbinary indicator of whether a barcode is associated with a nuclei (=1) or background (=0)
excluded_reasoncell callingbarcode categorization from the ATAC exclusion pipeline: 0 if barcode is not excluded; > 0 if excluded; 1 = more than 1 gel bead and a nuclei in a partition; 2 = low fraction of fragments overlapping peaks; 3 = barcode excluded because it was a multiplet
gex_raw_readssequencingtotal number of reads
gex_mapped_readsmappingnumber of reads that aligned to the reference genome
gex_conf_intergenic_readsmappingnumber of mapq 255 reads that are intergenic
gex_conf_exonic_readsmappingnumber of mapq 255 reads that are exonic
gex_conf_intronic_readsmappingnumber of mapq 255 reads that are intronic
gex_conf_exonic_unique_readsmappingnumber of mapq 255 reads that are exonic and map to only one gene in the sense orientation
gex_conf_exonic_antisense_readsmappingnumber of mapq 255 reads that are exonic and antisense
gex_conf_exonic_dup_readsmappingnumber of mapq 255 reads that are exonic, map to one gene, sense, are associated with a valid molecule, and are marked as duplicates
gex_exonic_umismappingnumber of mapq 255 reads that are exonic, map to one gene, sense, are associated with a valid molecule, and is the read representing that molecule
gex_conf_intronic_unique_readsmappingnumber of mapq 255 reads that are intronic and map to only one gene in the sense orientation (with --gex-exclude-introns this will always be zero)
gex_conf_intronic_antisense_readsmappingnumber of mapq 255 reads that are intronic and antisense (with --gex-exclude-introns this will always be zero)
gex_conf_intronic_dup_readsmappingnumber of mapq 255 reads that are intronic, map to one gene, sense, are associated with a valid molecule, and are marked as duplicates (with --gex-exclude-introns this will always be zero)
gex_intronic_umismappingnumber of mapq 255 reads that are intronic, map to one gene, sense, are associated with a valid molecule, and is the read representing that molecule (with --gex-exclude-introns this will always be zero)
gex_conf_txomic_unique_readsmappingnumber of mapq 255 reads that are exonic, sense, map to one gene, compatible with splice annotations, and are associated with a valid molecule
gex_umis_countsensitivitygex_intronic_umis + gex_exonic_umis
gex_genes_countsensitivitynumber of observed genes
atac_raw_readssequencingtotal number of read pairs
atac_unmapped_readsmappingnumber of read pairs with at least one end not mapped
atac_lowmapqmappingnumber of read pairs with <30 mapq on at least one end
atac_dup_readsmappingnumber of duplicate read pairs
atac_chimeric_readsmappingnumber of chimerically mapped read pairs
atac_mitochondrial_readsmappingnumber of read pairs mapping to mitochondria and other non-nuclear contigs
atac_fragmentssensitivitynumber of non-duplicate, usable read pairs that map to the nuclear genome
atac_TSS_fragmentstargetingnumber of fragments overlapping with TSS regions
atac_peak_region_fragmentstargetingnumber of fragments overlapping peaks
atac_peak_region_cutsitestargetingnumber of fragment ends that fall within peaks