Pipelines

Data Processing Pipelines QC Metrics

Overview

Here we provide the quality control metrics used to evaluate data quality for each data processing pipeline. Each metric is listed along with links to the tool used to perform that particular analysis and a description of the metric. If you want to submit a QC metric for addition to a pipeline or for feedback, please contact us at data-help@humancellatlas.org.

Smart-seq2 Pipeline Metrics

The Smart-seq2 pipeline processes data generated from plate-based Smart-seq2 scRNA sequencing protocols (full transcript). The metrics below are generated from the quality control module of the pipeline.

MetricProgramDetails
RnaSeqMetricsCollectRnaSeqMetricsMetrics Definitions
DuplicationMetricsMarkDuplicatesMetrics Definitions
AlignmentSummaryMetricsCollectMultipleMetricsMetrics Definitions
InsertSizeMetricsCollectMultipleMetricsMetrics Definitions
GcBiasMetrics,GcBiasDetailMetricsCollectMultipleMetricsMetrics Definitions
QualityYieldMetricsCollectMultipleMetricsMetrics Definitions
SequencingArtifactMetricsCollectMultipleMetricsMetrics Definitions

Optimus Pipeline Metrics

This pipeline processes genomic data generated from the 10x Genomics 3 prime v2 (and v3) assay. The metrics below are detected using Single Cell Tools (sctools).

Cell MetricsProgramDetails
n_readsSC ToolsThe number of reads associated with this entity. Metrics Definitions
noise_readsSC ToolsNumber 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_barcodesSC ToolsThe number of reads with molecule barcodes that have no errors. Metrics Definitions
reads_mapped_exonicSC ToolsThe number of reads for this entity that are mapped to exons. Metrics Definitions
reads_mapped_intronicSC ToolsThe number of reads for this entity that are mapped to introns. Metrics Definitions
reads_mapped_utrSC ToolsThe number of reads for this entity that are mapped to 3' untranslated regions (UTRs). Metrics Definitions
reads_mapped_uniquelySC ToolsThe number of reads mapped to a single unambiguous location in the genome. Metrics Definitions
reads_mapped_multipleSC ToolsThe number of reads mapped to multiple genomic positions with equal confidence. Metrics Definitions
duplicate_readsSC ToolsThe number of reads that are duplicates (see README.md for definition of a duplicate). Metrics Definitions
spliced_readsSC ToolsThe number of reads that overlap splicing junctions. Metrics Definitions
antisense_readsSC ToolsThe number of reads that are mapped to the antisense strand instead of the transcribed strand. Metrics Definitions
molecule_barcode_fraction_bases_above_30_meanSC ToolsThe 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_varianceSC ToolsThe 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_meanSC ToolsThe 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_varianceSC ToolsThe 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_meanSC ToolsAverage quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
genomic_read_quality_varianceSC ToolsVariance in quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
n_moleculesSC ToolsNumber of molecules corresponding to this entity. See README.md for the definition of a Molecule. Metrics Definitions
n_fragmentsSC ToolsNumber of fragments corresponding to this entity. See README.md for the definition of a Fragment. Metrics Definitions
reads_per_moleculeSC ToolsThe average number of reads associated with each molecule in this entity. Metrics Definitions
reads_per_fragmentSC ToolsThe average number of reads associated with each fragment in this entity. Metrics Definitions
fragments_per_moleculeSC ToolsThe average number of fragments associated with each molecule in this entity. Metrics Definitions
fragments_with_single_read_evidenceSC ToolsThe number of fragments associated with this entity that are observed by only one read. Metrics Definitions
molecules_with_single_read_evidenceSC ToolsThe number of molecules associated with this entity that are observed by only one read. Metrics Definitions
perfect_cell_barcodesSC ToolsThe number of reads whose cell barcodes contain no error. Metrics Definitions
reads_mapped_intergenicSC ToolsThe number of reads mapped to an intergenic region for this cell. Metrics Definitions
reads_mapped_too_many_lociSC ToolsThe 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_varianceSC ToolsThe 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_meanSC ToolsThe average fraction of Illumina base calls for the cell barcode sequence that are greater than 30, across molecules. Metrics Definitions
n_genesSC ToolsThe number of genes detected by this cell. Metrics Definitions
genes_detected_multiple_observationsSC ToolsThe number of genes that are observed by more than one read in this cell. Metrics Definitions
Gene MetricsProgramDetails
n_readsSC ToolsThe number of reads associated with this entity. Metrics Definitions
noise_readsSC ToolsNumber 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_barcodesSC ToolsThe number of reads with molecule barcodes that have no errors. Metrics Definitions
reads_mapped_exonicSC ToolsThe number of reads for this entity that are mapped to exons. Metrics Definitions
reads_mapped_intronicSC ToolsThe number of reads for this entity that are mapped to introns. Metrics Definitions
reads_mapped_utrSC ToolsThe number of reads for this entity that are mapped to 3' untranslated regions (UTRs). Metrics Definitions
reads_mapped_uniquelySC ToolsThe number of reads mapped to a single unambiguous location in the genome. Metrics Definitions
reads_mapped_multipleSC ToolsThe number of reads mapped to multiple genomic positions with equal confidence. Metrics Definitions
duplicate_readsSC ToolsThe number of reads that are duplicates (see README.md for definition of a duplicate). Metrics Definitions
spliced_readsSC ToolsThe number of reads that overlap splicing junctions. Metrics Definitions
antisense_readsSC ToolsThe number of reads that are mapped to the antisense strand instead of the transcribed strand. Metrics Definitions
molecule_barcode_fraction_bases_above_30_meanSC ToolsThe 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_varianceSC ToolsThe 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_meanSC ToolsThe 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_varianceSC ToolsThe 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_meanSC ToolsAverage quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
genomic_read_quality_varianceSC ToolsVariance in quality of Illumina base calls in the genomic reads corresponding to this entity. Metrics Definitions
n_moleculesSC ToolsNumber of molecules corresponding to this entity. See README.md for the definition of a Molecule. Metrics Definitions
n_fragmentsSC ToolsNumber of fragments corresponding to this entity. See README.md for the definition of a Fragment. Metrics Definitions
reads_per_moleculeSC ToolsThe average number of reads associated with each molecule in this entity. Metrics Definitions
reads_per_fragmentSC ToolsThe average number of reads associated with each fragment in this entity. Metrics Definitions
fragments_per_moleculeSC ToolsThe average number of fragments associated with each molecule in this entity. Metrics Definitions
fragments_with_single_read_evidenceSC ToolsThe number of fragments associated with this entity that are observed by only one read. Metrics Definitions
molecules_with_single_read_evidenceSC ToolsThe number of molecules associated with this entity that are observed by only one read. Metrics Definitions
number_cells_detected_multipleSC ToolsThe number of cells which observe more than one read of this gene. Metrics Definitions
number_cells_expressingSC ToolsThe number of cells that detect this gene. Metrics Definitions
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