Cell Ranger ARC2.0, printed on 12/03/2024
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.
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
| Metric | Type | Description |
|---|---|---|
barcode | key | barcode sequence associated with this data |
gex_barcode | key | Gene Expression library barcode sequence, identical to barcode |
atac_barcode | key | paired ATAC library barcode sequence |
is_cell | cell calling | binary indicator of whether a barcode is associated with a nuclei (=1) or background (=0) |
excluded_reason | cell calling | barcode 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_reads | sequencing | total number of reads |
gex_mapped_reads | mapping | number of reads that aligned to the reference genome |
gex_conf_intergenic_reads | mapping | number of mapq 255 reads that are intergenic |
gex_conf_exonic_reads | mapping | number of mapq 255 reads that are exonic |
gex_conf_intronic_reads | mapping | number of mapq 255 reads that are intronic |
gex_conf_exonic_unique_reads | mapping | number of mapq 255 reads that are exonic and map to only one gene in the sense orientation |
gex_conf_exonic_antisense_reads | mapping | number of mapq 255 reads that are exonic and antisense |
gex_conf_exonic_dup_reads | mapping | number 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_umis | mapping | number 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_reads | mapping | number 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_reads | mapping | number of mapq 255 reads that are intronic and antisense (with --gex-exclude-introns this will always be zero) |
gex_conf_intronic_dup_reads | mapping | number 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_umis | mapping | number 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_reads | mapping | number 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_count | sensitivity | gex_intronic_umis + gex_exonic_umis |
gex_genes_count | sensitivity | number of observed genes |
atac_raw_reads | sequencing | total number of read pairs |
atac_unmapped_reads | mapping | number of read pairs with at least one end not mapped |
atac_lowmapq | mapping | number of read pairs with <30 mapq on at least one end |
atac_dup_reads | mapping | number of duplicate read pairs |
atac_chimeric_reads | mapping | number of chimerically mapped read pairs |
atac_mitochondrial_reads | mapping | number of read pairs mapping to mitochondria and other non-nuclear contigs |
atac_fragments | sensitivity | number of non-duplicate, usable read pairs that map to the nuclear genome |
atac_TSS_fragments | targeting | number of fragments overlapping with TSS regions |
atac_peak_region_fragments | targeting | number of fragments overlapping peaks |
atac_peak_region_cutsites | targeting | number of fragment ends that fall within peaks |