Skip to content

Barcodes Output

The barcodes directory contains barcode demultiplexing results and detailed metrics for each library in the analysis. To publish sample demultiplexed unaligned BAM files in the barcodes directory, set --bcParserBamOut to true.

Important

The contents of the barcodes folder are not necessary to review unless users are troubleshooting barcode error rates or general barcode troubleshooting. All of these metrics are avialiable and accumulated in both the "library" and "sample" level reports (see here), however, the raw data as well as unaligned sample specific bam files will be located here.

Directory Structure

barcodes
├── QSR-P.metrics.json
└── split_bcparser_jobs
    ├── bcparser.QSR-P.1
    │   └── QSR-P.demux
    │       ├── barcode_counts.PBC.tsv
    │       ├── barcode_counts.PCR.tsv
    │       ├── barcode_counts.bead1.tsv
    │       ├── barcode_counts.bead2.tsv
    │       ├── barcode_counts.bead3.tsv
    │       ├── barcode_counts.umi.tsv
    │       └── metrics.json
    ├── bcparser.QSR-P.2
    │   └── QSR-P.demux
    │       ├── barcode_counts.PBC.tsv
    │       ├── barcode_counts.PCR.tsv
    │       ├── barcode_counts.bead1.tsv
    │       ├── barcode_counts.bead2.tsv
    │       ├── barcode_counts.bead3.tsv
    │       ├── barcode_counts.umi.tsv
    │       └── metrics.json
    └── ... (additional split jobs)

Key Files and Directories

Library Metrics (*.metrics.json)

Comprehensive JSON file containing library-wide barcode demultiplexing statistics:

  • Total reads processed
  • Barcode error rates by type
  • Sample assignment statistics

Parallel Processing Jobs (split_bcparser_jobs/)

The barcode parsing is performed in parallel across multiple jobs. Each job directory contains:

Job Results (bcparser.*.*/)

Contains the demultiplexing results for a specific job chunk.

Demultiplexing Data (demux/)

Contains detailed barcode count files for each barcode type:

Pooled Barcode Counts (PBC) (barcode_counts.PBC.tsv)

  • RT pool barcode counts and statistics
  • Sample assignment information
  • Error rates and quality metrics

Library Barcode Counts (PCR) (barcode_counts.PCR.tsv)

  • PCR barcode detection results
  • Library identification metrics
  • Quality scores and error rates

Bead Barcode Counts (barcode_counts.bead*.tsv)

  • Individual bead barcode statistics
  • Microwell identification results
  • Error correction metrics

UMI Statistics (barcode_counts.umi.tsv)

  • UMI (Unique Molecular Identifier) statistics
  • Duplicate detection metrics
  • Quality assessment data

Job Metrics (metrics.json)

  • Job-specific demultiplexing metrics
  • Processing statistics
  • Error rates and quality scores

TSV Files (barcode_counts.*.tsv)

Tab-separated files containing:

  • Barcode sequence
  • Count/frequency
  • Quality metrics
  • Error rates
  • Sample assignments

JSON Files (metrics.json)

Structured data containing:

  • Total reads processed
  • Sample assignment results

Need Help?

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