Loom_schema_OUTDATED.md

What's in the Optimus Pipeline Loom File?

The Loom file is an HDF5 file generated using Loompy v.2.0.17. It contains UMI-corrected counts as well as multiple metrics for both individual cells (the columns of the matrix; Table 1) and individual genes (the rows of the matrix; Table 2). The tables below document these metrics, list which tools generate them, and define them. This Loom file is an optional output of the Optimus pipeline. The default matrix output of the Optimus pipeline is a ZARR Array. The Loom file is directly derived from the ZARR and contains the same information with only minor header updates for schema compatibility.

Note: Loom files generated by Optimus are different from the final Loom file distributed on the Human Cell Atlas Data Portal, which removes some of the metadata detailed in this document and contains additional metadata relating to each individual project.

Table 1. Column Attributes (Cell Metrics)

Cell Metrics	Program	Details
CellID	SC Tools	The unique identifier for each cell based on 10X Cell Barcodes
n_reads	SC Tools	The number of reads associated with this entity. Metrics Definitions
noise_reads	SC Tools	Number of reads that are categorized by 10x Genomics Cell Ranger as "noise". Refers to long polymers, or reads with high numbers of N (ambiguous) nucleotides. Metrics Definitions
perfect_molecule_barcodes	SC Tools	The number of reads with molecule barcodes that have no errors. Metrics Definitions
reads_mapped_exonic	SC Tools	The number of reads for this entity that are mapped to exons. Metrics Definitions
reads_mapped_intronic	SC Tools	The number of reads for this entity that are mapped to introns. Metrics Definitions
reads_mapped_utr	SC Tools	The number of reads for this entity that are mapped to 3' untranslated regions (UTRs). Metrics Definitions
reads_mapped_uniquely	SC Tools	The number of reads mapped to a single unambiguous location in the genome. Metrics Definitions
reads_mapped_multiple	SC Tools	The number of reads mapped to multiple genomic positions with equal confidence. Metrics Definitions
duplicate_reads	SC Tools	The number of reads that are duplicates (see README.md for definition of a duplicate). Metrics Definitions
spliced_reads	SC Tools	The number of reads that overlap splicing junctions. Metrics Definitions
antisense_reads	SC Tools	The number of reads that are mapped to the antisense strand instead of the transcribed strand. Metrics Definitions
molecule_barcode_fraction_bases_above_30_mean	SC Tools	The average fraction of bases in molecule barcodes that receive quality scores greater than 30 across the reads of this entity. Metrics Definitions
molecule_barcode_fraction_bases_above_30_variance	SC Tools	The variance in the fraction of bases in molecule barcodes that receive quality scores greater than 30 across the reads of this entity. Metrics Definitions
genomic_reads_fraction_bases_quality_above_30_mean	SC Tools	The average fraction of bases in the genomic read that receive quality scores greater than 30 across the reads of this entity (included for 10x Cell Ranger count comparison). Metrics Definitions
genomic_reads_fraction_bases_quality_above_30_variance	SC Tools	The variance in the fraction of bases in the genomic read that receive quality scores greater than 30 across the reads of this entity (included for 10x Cell Ranger count comparison). Metrics Definitions
genomic_read_quality_mean	SC Tools	Average quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
genomic_read_quality_variance	SC Tools	Variance in quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
n_molecules	SC Tools	Number of molecules corresponding to this entity. See README.md for the definition of a Molecule. Metrics Definitions
n_fragments	SC Tools	Number of fragments corresponding to this entity. See README.md for the definition of a Fragment. Metrics Definitions
reads_per_fragment	SC Tools	The average number of reads associated with each fragment in this entity. Metrics Definitions
fragments_per_molecule	SC Tools	The average number of fragments associated with each molecule in this entity. Metrics Definitions
fragments_with_single_read_evidence	SC Tools	The number of fragments associated with this entity that are observed by only one read. Metrics Definitions
molecules_with_single_read_evidence	SC Tools	The number of molecules associated with this entity that are observed by only one read. Metrics Definitions
perfect_cell_barcodes	SC Tools	The number of reads whose cell barcodes contain no error. Metrics Definitions
reads_mapped_intergenic	SC Tools	The number of reads mapped to an intergenic region for this cell. Metrics Definitions
reads_mapped_too_many_loci	SC Tools	The number of reads that were mapped to too many loci across the genome and as a consequence, are reported unmapped by the aligner. Metrics Definitions
cell_barcode_fraction_bases_above_30_variance	SC Tools	The variance of the fraction of Illumina base calls for the cell barcode sequence that are greater than 30, across molecules. Metrics Definitions
cell_barcode_fraction_bases_above_30_mean	SC Tools	The average fraction of Illumina base calls for the cell barcode sequences that are greater than 30, across molecules. Metrics Definitions
n_genes	SC Tools	The number of genes detected by this cell. Metrics Definitions
genes_detected_multiple_observations	SC Tools	The number of genes that are observed by more than one read in this cell. Metrics Definitions
reads_unmapped	SC Tools	Reads that are non-transcriptomic
emptydrops_FDR	dropletUtils	False Discovery Rate (FDR) for being a non-empty droplet
emptydrops_IsCell	dropletUtils	Binarized call of cell/background based on predefined FDR cutoff
emptydrops_Limited	dropletUtils	Indicates whether a lower p-value could be obtained by increasing the number of iterations
emptydrops_LogProb	dropletUtils	The log-probability of observing the barcode’s count vector under the null model
emptydrops_PValue	dropletUtils	Numeric, the Monte Carlo p-value against the null model
emptydrops_Total	dropletUtils	Numeric, the total read counts for each barcode

Table 2. Row Attributes (Gene Metrics)

Gene Metrics	Program	Details
Accession	GENCODE GTF	The gene_id listed in the GENCODE GTF
Gene	GENCODE GTF	The unique gene_name provided in the GENCODE GTF
n_reads	SC Tools	The number of reads associated with this entity. Metrics Definitions
noise_reads	SC Tools	Number of reads that are categorized by 10x Genomics Cell Ranger as "noise". Refers to long polymers, or reads with high numbers of N (ambiguous) nucleotides. Metrics Definitions
perfect_molecule_barcodes	SC Tools	The number of reads with molecule barcodes that have no errors. Metrics Definitions
reads_mapped_exonic	SC Tools	The number of reads for this entity that are mapped to exons. Metrics Definitions
reads_mapped_intronic	SC Tools	The number of reads for this entity that are mapped to introns. Metrics Definitions
reads_mapped_utr	SC Tools	The number of reads for this entity that are mapped to 3' untranslated regions (UTRs). Metrics Definitions
reads_mapped_uniquely	SC Tools	The number of reads mapped to a single unambiguous location in the genome. Metrics Definitions
reads_mapped_multiple	SC Tools	The number of reads mapped to multiple genomic positions with equal confidence. Metrics Definitions
duplicate_reads	SC Tools	The number of reads that are duplicates (see README.md for definition of a duplicate). Metrics Definitions
spliced_reads	SC Tools	The number of reads that overlap splicing junctions. Metrics Definitions
antisense_reads	SC Tools	The number of reads that are mapped to the antisense strand instead of the transcribed strand. Metrics Definitions
molecule_barcode_fraction_bases_above_30_mean	SC Tools	The average fraction of bases in molecule barcodes that receive quality scores greater than 30 across the reads of this entity. Metrics Definitions
molecule_barcode_fraction_bases_above_30_variance	SC Tools	The variance in the fraction of bases in molecule barcodes that receive quality scores greater than 30 across the reads of this entity. Metrics Definitions
genomic_reads_fraction_bases_quality_above_30_mean	SC Tools	The average fraction of bases in the genomic read that receive quality scores greater than 30 across the reads of this entity (included for 10x Cell Ranger count comparison). Metrics Definitions
genomic_reads_fraction_bases_quality_above_30_variance	SC Tools	The variance in the fraction of bases in the genomic read that receive quality scores greater than 30 across the reads of this entity (included for 10x Cell Ranger count comparison). Metrics Definitions
genomic_read_quality_mean	SC Tools	Average quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
genomic_read_quality_variance	SC Tools	Variance in quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
n_molecules	SC Tools	Number of molecules corresponding to this entity. See README.md for the definition of a Molecule. Metrics Definitions
n_fragments	SC Tools	Number of fragments corresponding to this entity. See README.md for the definition of a Fragment. Metrics Definitions
reads_per_molecule	SC Tools	The average number of reads associated with each molecule in this entity. Metrics Definitions
reads_per_fragment	SC Tools	The average number of reads associated with each fragment in this entity. Metrics Definitions
fragments_per_molecule	SC Tools	The average number of fragments associated with each molecule in this entity. Metrics Definitions
fragments_with_single_read_evidence	SC Tools	The number of fragments associated with this entity that are observed by only one read. Metrics Definitions
molecules_with_single_read_evidence	SC Tools	The number of molecules associated with this entity that are observed by only one read. Metrics Definitions
number_cells_detected_multiple	SC Tools	The number of cells which observe more than one read of this gene. Metrics Definitions
number_cells_expressing	SC Tools	The number of cells that detect this gene. Metrics Definitions