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DRAGEN Single Cell RNA
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DRAGEN Single Cell RNA
  • Introduction
  • Get Started
    • Prerequisites
  • Run Set Up
    • Sample Sheet Introduction
    • Run Planning in BaseSpace Sequence Hub
    • Sample Sheet Requirements
    • Manual Launch on BaseSpace
  • Analysis Methods
    • FASTQ Processing
    • Error Correction
    • Transcript Counting
    • PIPseq CRISPR Mode
  • Analysis Results
    • Accessing Results
    • DRAGEN Report
      • Single-Cell RNA
      • Single-Cell Clustering
      • Trimmer
      • DRAGEN FastQC
      • Mapping
    • Secondary Analysis Results
  • Tertiary Analysis
    • Illumina Connected Multiomics
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  • Read-Level Metrics
  • Base-Level Metrics
  • Deduplication
  • Read MAPQs

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  1. Analysis Results
  2. DRAGEN Report

Mapping

Read-Level Metrics

Metric
Description

Total input reads

Total number of input reads

QC-failed reads

Total number of reads failing one or more quality checks

% QC-failed

Percentage of reads failing one or more quality checks

Unique reads

Total number of unique reads

% Unique

Percentage of reads that are unique

Mapped reads

Total number of mapped reads, adjusted for filtered and excluded targets

% Mapped

Percentage of reads that are mapped, adjusted for filtered and excluded targets

Base-Level Metrics

Metric
Description

Total Bases

Total number of input bases

Mapped R1

Total number of mapped bases on R1

% Mapped R1

Percentage of R1 bases mapped

% Q30 R1

Percentage of R1 bases with phred quality score >=30

Deduplication

The deduplication bar chart reflects the ratio of unique and deduplicated reads.

Read MAPQs

The read MAPQs bar chart reflects the percent of reads in various categories of phred quality score (Q0-Q10, Q10-Q20, Q20-Q30, Q30-Q40, Q40+).

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Last updated 4 months ago

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