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QC Reports

The ScaleRna workflow generates quality control reports at both the library and sample levels. These reports help you assess data quality, troubleshoot issues, and understand your single-cell RNA-seq results.

Report Overview

Report Types

Library Report (library_{LibraryName}.report.html)

  • Provides sequencing, barcode, and demultiplexing information for all samples in one run and represents the entire library
  • Shows overall library performance and barcode success rates

Sample Report ({SampleName}.{LibraryName}.report.html) - Contains detailed metrics and plots for individual biological samples - Focuses on cell-level analysis and quality metrics

MultiQC Report (multiqc_report.html) - Comprehensive summary of all FastQC results - Batch analysis of sequencing quality across all samples

Directory Structure

reports/
├── library/                           # Library-level reports
│   ├── csv/                          # Library CSV data
│   │   ├── library_QSR-P.overallMatches.csv
│   │   ├── library_QSR-P.typeLevelMatches.csv
│   │   ├── library_QSR-P_unique_reads_PBC_well.csv
│   │   ├── library_QSR-P-SCALEPLEX.overallMatches.csv
│   │   ├── library_QSR-P-SCALEPLEX.typeLevelMatches.csv
│   │   └── library_QSR-P-SCALEPLEX_unique_reads_PBC_well.csv
│   ├── library_QSR-P.report.html            # Main library report
│   └── library_QSR-P-SCALEPLEX.report.html  # ScalePlex library report
├── csv/                              # Sample-level CSV data
│   ├── QS-SmallKit-PBMCs.QSR-P.reportStatistics.csv
│   ├── QS-SmallKit-PBMCs.QSR-P_num_cells_by_PBC_Index_well.csv
│   ├── QS-SmallKit-PBMCs.QSR-P_unique_transcript_counts_by_PBC_Index_well.csv
│   ├── QS-SmallKit-PBMCs.QSR-P-SCALEPLEX.scaleplex_stats.csv
│   └── reads_per_sample.csv
├── QS-SmallKit-PBMCs.QSR-P.report.html      # Sample report
├── allSamples.reportStatistics.csv          # Combined statistics
└── multiqc_report.html                      # MultiQC summary

Key Metrics Explained

Library-Level Metrics

Read Status:

  • Pass: Reads with all expected barcodes found ✅
  • BarcodeError: Reads with unmatched barcodes ❌
  • TooShortError: Reads <16 bases after trimming ⚠️

Barcode Performance:

  • Exact: Perfect barcode matches
  • Corrected: Barcodes corrected by error correction (default allows 1 bp mismatch)
  • NoMatch: Barcodes that couldn't be matched

Sample-Level Metrics

Read Quality:

  • Total Sample Reads: Reads assigned to sample after barcode filtering
  • Reads Mapped to Genome: Fraction aligned to reference genome
  • Exonic Reads: Fraction overlapping exons (expected RNA signal)
  • Antisense Reads: Fraction in antisense direction (potential contamination)
  • Mitochondrial Reads: Fraction mapping to mitochondrial genome (cell quality indicator)

Cell Quality:

  • Cells Called: Number of cell barcodes passing filters
  • Reads per Cell: Average sequencing depth per cell
  • Median UTCs: Median unique transcript counts per cell
  • Median Genes: Median genes detected per cell
  • Reads in Cells: Fraction of reads in cells vs background

Complexity Analysis:

  • Shows transcript counts at different sequencing depths
  • Helps determine if more sequencing is needed
  • Should approach plateau at higher read counts

CSV Data Files

Library CSV Files

library_QSR-P.overallMatches.csv

Status,Reads,Percent
Pass,5179020483,85.8%
BarcodeError,604806544,10.0%
TooShortError,254739737,4.2%

library_QSR-P.typeLevelMatches.csv

Barcode,Match,Reads
PCR,Exact,100.0%
bead1,Exact,98.2%
PBC,Exact,93.3%

Sample CSV Files

QS-SmallKit-PBMCs.QSR-P.reportStatistics.csv

Contains comprehensive sample statistics including read metrics, cell metrics, complexity analysis, and ScalePlex metrics.

QS-SmallKit-PBMCs.QSR-P_num_cells_by_PBC_Index_well.csv

Plate-map showing number of cells called per RT well.

QS-SmallKit-PBMCs.QSR-P_unique_transcript_counts_by_PBC_Index_well.csv

Plate-map showing median transcript counts per RT well.

Need Help?

For more information, please contact support@scale.bio or visit our support website.